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At least 415 records · Page 23

Automated electrosynthesis reaction mining with multimodal large language models (MLLMs)

Leveraging the chemical data available in legacy formats such as publications and patents is a significant challenge for the community. Automated reaction mining offers a promising solution to unleash this knowledge into a learnable digital form and therefore help expedite materials and reaction discovery. However, existing reaction mining toolkits are limited to single input modalities (text or images) and cannot effectively integrate heterogeneous data that is scattered across text, tables, and figures. In this work, we go beyond single input modalities and explore multimodal large language models (MLLMs) for the analysis of diverse data inputs for automated electrosynthesis reaction mining. We compiled a test dataset of 65 articles (MERMES-T24 set) and employed it to benchmark five prominent MLLMs against two critical tasks: (i) reaction diagram parsing and (ii) resolving cross-modality data interdependencies. The frontrunner MLLM achieved ≥96% accuracy in both tasks, with the strategic integration of single-shot visual prompts and image pre-processing techniques. We integrate this capability into a toolkit named MERMES (multimodal reaction mining pipeline for electrosynthesis). Our toolkit functions as an end-to-end MLLM-powered pipeline that integrates article retrieval, information extraction and multimodal analysis for streamlining and automating knowledge extraction. This work lays the groundwork for the increased utilization of MLLMs to accelerate the digitization of chemistry knowledge for data-driven research.

Leong, Shi Xuan↗

Computing chemical potentials with machine-learning-accelerated simulations to accurately predict thermodynamic properties of molten salts

The successful design and deployment of next-generation nuclear technologies heavily rely on thermodynamic data for relevant molten salt systems. However, the lack of accurate force fields and efficient methods has limited the quality of thermodynamic predictions from atomistic simulations. Here we propose an efficient free energy framework for computing chemical potentials, which is the central free energy quantity behind many thermodynamic properties. We accelerate our simulations without sacrificing accuracy by using machine learning interatomic potentials trained on density functional theory (DFT) data. Using lithium chloride as our model system, we compute chemical potentials with DFT-accuracy for solid and liquid phases by transmuting ions into noninteracting particles. Notably, in the liquid phase, we demonstrate consistency whether we transmute one ion pair or the entire system into ideal gas particles. By locating the temperature where the chemical potential of solid and liquid phases cross, we predict a melting point of 880 ± 18 K for lithium chloride, which is remarkably close to the experimental value of 883 K. With this successful demonstration, we lay the foundation for high-throughput thermodynamic predictions of many properties that can be derived from the chemical potentials of the minority and majority components in molten salts.

Gibson, Luke D. [Oak Ridge National Laboratory (OR↗

Computational insights into hydrogen adsorption energies on medium-entropy oxides

High entropy oxides (HEOs) have emerged as promising catalysts for several important chemical transformations including alkane activation. Hydrogen adsorption energy (HAE) has been used as a key descriptor for many reactions including methane C–H activation and hydrogen evolution reactions. Hence, understanding the relationship between HAEs and the surface chemistry of HEO surfaces could lay the foundation for meaningful correlations among methane C–H activation, HAE, and the complex, local environment of HEO surfaces. Here, we used a medium-entropy oxide as a prototypical system – Mg 0.25 Ni 0.25 Cu 0.25 Zn 0.25 O with a rock-salt structure – to interrogate these relationships. We sampled 2000 different surfaces of its (100) plane and calculated the HAEs at randomly chosen surface O sites using density functional theory (DFT). Our analysis of the 2000 data points reveals that the HAEs at the surface O sites are significantly influenced by the local environment around the adsorption sites, particularly the nature of the metal atom directly below the surface O site where H adsorbs. After comparing several popular graph-neural-network-based machine learning models, we found that the DimeNet++ model performed best achieving satisfactory accuracy in predicting HAEs for both Mg 0.25 Ni 0.25 Cu 0.25 Zn 0.25 O and slightly varied compositions. Our work underscores the promise of such models and the need for further refinement to address the complexity of HEOs.

Song, Haohong [Vanderbilt Univ., Nashville, TN (Un↗

ToPolyAgent: AI agents for coarse-grained bead-spring topological polymer simulations

We introduce ToPolyAgent, a multi-agent AI framework for performing coarse-grained molecular dynamics (MD) simulations of topological polymers through natural language instructions. By integrating large language models (LLMs) with domain-specific computational tools, ToPolyAgent supports both interactive and autonomous simulation workflows across diverse polymer architectures, including linear, ring, brush, and star polymers, as well as dendrimers. The system consists of four LLM-powered agents: a Config Agent for generating initial polymer–solvent configurations, a Simulation Agent for executing LAMMPS-based MD simulations and conformational analyses, a Report Agent for compiling markdown reports, and a Workflow Agent for streamlined autonomous operations. Interactive mode incorporates user feedback loops for iterative refinements, while autonomous mode enables end-to-end task execution from detailed prompts. We demonstrate ToPolyAgent's versatility through case studies involving diverse polymer architectures under varying solvent conditions, thermostats, and simulation lengths. Furthermore, we highlight its potential as a research assistant by directing it to investigate the effect of interaction parameters on the linear polymer conformation, and the influence of grafting density on the persistence length of the brush polymer. By coupling natural language interfaces with rigorous simulation tools, ToPolyAgent lowers barriers to complex computational workflows and advances AI-driven materials discovery in polymer science. It lays the foundation for autonomous and extensible multi-agent scientific research ecosystems.

Ding, Lijie [Oak Ridge National Laboratory (ORNL),↗

Side-chain ionization enables ultrafast intramolecular singlet fission in the azaquinodimethane skeleton

Singlet fission (SF) could significantly alleviate thermalization losses of high-energy photons, thus holding great potential for improving the power conversion efficiency of solar cells. Conventional SF materials require an intricate control of molecular packing motifs in the solid state to achieve efficient multiexciton generation. Small molecule intramolecular singlet fission (iSF) materials have emerged as promising alternatives and show great potential for practical device applications. However, the scope of such iSF materials remains rather limited, necessitating innovative molecular design strategies. Herein, we present how a side-chain ionization strategy leads to an iSF chromophore based on the azaquinodimethane (AQM) ring system. Systematic theoretical and spectroscopic analyses reveal that the direct attachment of electron-withdrawing ionic groups to the conjugated AQM core renders the originally fluorescent AQM nonemissive, leading to ionic AQM (iAQM) derivatives capable of ultrafast iSF to populate triplet-like species. Further fine-tuning of the iAQM skeleton imparts subtle intermolecular interactions that are indispensable for the efficient separation of triplet pairs following iSF in the aggregated state. Our findings offer unprecedented insights into molecular design and triplet exciton dynamics, laying the foundation for the discovery of rare molecular iSF materials.

Wu, Zixiang↗

Microstructure of amide-functionalized polyethylenes determined by NMR relaxometry

Amidation of polyethylenes creates a range of amide-containing materials with enhanced properties, but the effect of these functional groups on the microstructure of these new materials is not known. Here we employ solid-state nuclear magnetic resonance (NMR) techniques to analyze the microstructure of amide-modified polyethylenes. While a decrease in crystallinity was observed with increasing amounts of functionalization, we found by measuring the chain mobility of the crystalline, amorphous, and interphasial regions of the polyethylenes with NMR relaxation techniques that the grafted amidyl groups partition into the rigid amorphous fraction (RAF) between the crystalline and amorphous regions. The chemical specificity of these NMR experiments creates precise assessments of the location of functional groups within the materials. Together, these insights into the microstructure and morphology of amide-containing polyethylenes lay a foundation for a deeper understanding of the structure and properties of functional polyolefins.

Haber, Shira [Lawrence Berkeley National Laborator↗

Photo-Swing CO2 Capture Using a Branched Polyethylenimine As Sorbents and TiN Light Absorber

Using branched polyethylenimine as the sorbent material for dilute CO2 capture, a photo-swing method is demonstrated in an industrially relevant support architecture using titanium nitride (TiN) nanosized light absorbers coupled with low-power LEDs with irradiances up to 420 mW cm-2. The photo-swing desorption process is applied to dry and humid streams of 400 ppm CO2 diluted in N2. Consistent with known sorption mechanisms for aminopolymers, humid CO2 streams increased the CO2 uptake, in our case by ~30%. The photo-swing CO2 capture desorbed ~83% and ~100% CO2 compared to thermally-driven desorption over the same period for a dry and humid CO2 stream, respectively. The photo-swing CO2 capture exhibits robust performance over >90 cycles without significant signs of photo(thermal) induced sorbent degradation. This work lays the groundwork for photo-swing DAC technology as a scalable, energy-efficient solution for CO2 capture, well-suited for modular systems in remote locations utilizing intermittent renewable energy sources.

36 MATERIALS SCIENCE↗

Efficiently predicting pressure-composition-temperature diagrams to discover low-stability metal hydrides

Quantitatively accurate computational predictions of metal hydride thermodynamics are challenging but critical for alloy performance optimization across a multitude of technological domains, including hydrogen storage, compression, purification, and getters. Recent machine learning approaches have demonstrated great success in this area, but can potentially suffer from several shortcomings since they rely on imbalanced experimental training data and can have poor out-of-distribution (ood) test performance. Here, in this study, we circumvent such pitfalls by developing a computationally efficient, first principles-based workflow for direct prediction of metal hydride phase equilibrium, i.e., the pressure-composition-temperature (PCT) diagram. We then demonstrate its utility on predicting low stability hydrides derived from compositionally complex C14 Laves phase AB2 alloys. Specifically, we computationally predict and then experimentally validate an AB 2 alloy series (z < 0.6 for Ti 2−z Zr z CrMnFeNi) with ideal hydriding thermodynamics for a two-stage metal hydride-based compressor for pressurizing boil off from liquefied hydrogen. Importantly, this study lays the groundwork for accurate and efficient discovery/optimization of ood, low-stability hydrides for which purely data-driven approaches lack sufficient accuracy.

08 HYDROGEN↗

Gaunt and Breit two-electron contributions to mean-field transformations and fine structure splitting

Materials utilized by novel energy systems are often studied using weakly correlated mean-field theories. However, if these systems incorporate heavy elements, relativistic effects must be included. Therefore, a Kramers unrestricted coupled cluster with singles and doubles excitation formalism within a molecular mean-field exact two-component framework (X2C mmf ) using a four-component Dirac–Hartree–Fock (DHF) reference state is presented. The exact X2C mmf transformed normal-order Hamiltonian incorporates all one-electron and two-electron (2e) contributions from the Coulomb, Gaunt, and Breit operators and is used with the equation of motion method to calculate the excitation energies of the alkali group of elements. Using this framework, the effects of 2e Gaunt and Breit integrals are studied. Results demonstrate growing contributions from these integrals to the generated X2C mmf mean-fields and electronic fine structure calculations with increasing atomic number. Overall, this paper outlines the method, its effect within the X2C mmf approach, and lays the foundation for future theoretical development of relativistic calculations within this framework.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Gene editing and CRISPR in the clinic: current and future perspectives

Genome editing technologies, particularly those based on zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeat DNA sequences)/Cas9 are rapidly progressing into clinical trials. Most clinical use of CRISPR to date has focused on ex vivo gene editing of cells followed by their re-introduction back into the patient. The ex vivo editing approach is highly effective for many disease states, including cancers and sickle cell disease, but ideally genome editing would also be applied to diseases which require cell modification in vivo. However, in vivo use of CRISPR technologies can be confounded by problems such as off-target editing, inefficient or off-target delivery, and stimulation of counterproductive immune responses. Current research addressing these issues may provide new opportunities for use of CRISPR in the clinical space. In this review, we examine the current status and scientific basis of clinical trials featuring ZFNs, TALENs, and CRISPR-based genome editing, the known limitations of CRISPR use in humans, and the rapidly developing CRISPR engineering space that should lay the groundwork for further translation to clinical application.

59 BASIC BIOLOGICAL SCIENCES↗

Measuring the giant radio galaxy length distribution with the LoTSS

Many massive galaxies launch jets from the accretion disk of their central black hole, but only ~10 3 instances are known in which the associated outflows form giant radio galaxies (GRGs, or giants): luminous structures of megaparsec extent that consist of atomic nuclei, relativistic electrons, and magnetic fields. Large samples are imperative to understanding the enigmatic growth of giants, and recent systematic searches in homogeneous surveys constitute a promising development. For the first time, it is possible to perform meaningful precision statistics with GRG lengths, but a framework to do so is missing. We measured the intrinsic GRG length distribution by combining a novel statistical framework with a LOFAR Two-metre Sky Survey (LoTSS) sample of freshly discovered giants. In turn, this allowed us to answer an array of questions on giants. For example, we can now assess how rare a 5 Mpc giant is compared with one of 1 Mpc, and how much larger – given a projected length – the corresponding intrinsic length is expected to be. Notably, we can now also infer the GRG number density in the Local Universe. We assumed the intrinsic GRG length distribution to be Paretian (i.e. of power-law form) with tail index ξ, and predicted the observed distribution by modelling projection and selection effects. To infer ξ, we also systematically searched the LoTSS for hitherto unknown giants and compiled the largest catalogue of giants to date. We show that if intrinsic GRG lengths are Pareto distributed with index ξ, then projected GRG lengths are also Pareto distributed with index ξ. Selection effects induce curvature in the observed projected GRG length distribution: angular length selection flattens it towards the lower end, while surface brightness selection steepens it towards the higher end. We explicitly derived a GRG’s posterior over intrinsic lengths given its projected length, laying bare the ξ dependence. We also discovered 2060 giants within LoTSS DR2 pipeline products; our sample more than doubles the known population. Spectacular discoveries include the largest, second-largest, and fourth-largest GRG known (l p = 5.1 Mpc, l p = 5.0 Mpc, and l p = 4.8 Mpc), the largest GRG known hosted by a spiral galaxy (l p = 2.5 Mpc), and the largest secure GRG known beyond redshift 1 (l p = 3.9 Mpc). We increase the number of known giants whose angular length exceeds that of the Moon from 10 to 23; among the discoveries is the angularly largest known radio galaxy in the Northern Sky, which is also the angularly largest known GRG ($\phi$ = 2°). Combining theory and data, we determined that intrinsic GRG lengths are well described by a Pareto distribution, and measured the index ξ = –3.5 ± 0.5. This implies that, given its projected length, a GRG’s intrinsic length is expected to be just 15% larger. Finally, we determined the comoving number density of giants in the Local Universe to be n GRG = 5 ± 2(100 Mpc) –3 . We developed a practical mathematical framework that elucidates the statistics of giant radio galaxy lengths. Through a LoTSS search, we also discovered 2060 new giants. By combining both advances, we determined that intrinsic GRG lengths are well described by a Pareto distribution with index ξ = –3.5 ± 0.5, and that giants are truly rare in a cosmological sense: most clusters and filaments of the Cosmic Web are not currently home to a giant. Thus, our work yields new observational constraints for analytical models and simulations featuring radio galaxy growth.

79 ASTRONOMY AND ASTROPHYSICS↗

In-depth analysis of solar models with high-metallicity abundances and updated opacity tables

Context. As a result of the high-quality constraints available for the Sun, we are able to carry out detailed combined analyses using neutrino, spectroscopic, and helioseismic observations. These studies lay the ground for future improvements of the key physical components of solar and stellar models because ingredients such as the equation of state, the radiative opacities, or the prescriptions for macroscopic transport processes of chemicals are then used to study other stars in the Universe. Aims. We study the existing degeneracies in solar models using the recent high-metallicity spectroscopic abundances by comparing them to helioseismic and neutrino data and discuss the effect on their properties of changes in the micro and macro physical ingredients. Methods. We carried out a detailed study of solar models computed with a high-metallicity composition from the literature based on averaged 3D models that were claimed to resolve the solar modelling problem. We compared these models to helioseismic and neutrino constraints. Results. The properties of the solar models are significantly affected by the use of the recent OPLIB opacity tables and the inclusion of macroscopic transport. The properties of the standard solar models computed using the OPAL opacities are similar to those for which the OP opacities were used. We show that a modification of the temperature gradient just below the base of the convective zone is required to remove the discrepancies in solar models, particularly in the presence of macroscopic mixing. This can be simulated by a localised increase in the opacity of a few percent. Conclusions. We conclude that the existing degeneracies and issues in solar modelling are not removed by using an increase in the solar metallicity, in contradiction to what has been suggested in the recent literature. Therefore, standard solar models cannot be used as an argument for a high-metallicity composition. While further work is required to improve solar models, we note that direct helioseismic inversions indicate a low metallicity in the convective envelope, in agreement with spectroscopic analyses based on full 3D models.

74 ATOMIC AND MOLECULAR PHYSICS↗

Generalized framework for likelihood-based field-level inference of growth rate from velocity and density fields

Measuring the growth rate of large-scale structures ( f ) as a function of redshift has the potential to break degeneracies between modified gravity and dark energy models, when combined with expansion-rate probes. Direct estimates of peculiar velocities of galaxies have attracted interest as a means of estimating fσ 8 . In particular, field-level methods can be used to fit the field nuisance parameter along with cosmological parameters simultaneously. This article aims to provide the community with a unified framework for the theoretical modeling of the likelihood-based field-level inference by performing fast field covariance calculations for velocity and density fields. Our purpose is to lay the foundations for a nonlinear extension of the likelihood-based method at the field level. We have developed a generalized framework, implemented in the dedicated software flip to perform a likelihood-based inference of fσ 8 . We derived a new field covariance model, which includes wide-angle corrections. We also included the models previously described in the literature inside our framework. We compared their performance against ours, and we validated our model by comparing it with the two-point statistics of a recent N-body simulation. The tests we performed have allowed us to validate our software and determine the appropriate wavenumber range to integrate our covariance model and its validity in terms of separation. Our framework allows for a wider wavenumber coverage to be used in our calculations than in previous works, which is particularly interesting for nonlinear model extensions. Finally, our generalized framework allows us to efficiently perform a survey geometry-dependent Fisher forecast of the fσ 8 parameter. We show that the Fisher forecast method we developed gives an error bar that is 30% closer to a full likelihood-based estimation than a standard volume Fisher forecast.

Ravoux, Corentin↗

Electric dipole excitations near the neutron separation energies in 96 Mo

Electric dipole strength near the neutron separation energy significantly impacts nuclear structure properties and astrophysical scenarios. These excitations are complex in nature and may involve the so-called pygmy dipole resonance (PDR). Transition densities play a crucial role in understanding the nature of nuclear excited states, including collective excitations, as well as in constructing transition potentials in DWBA or coupled-channels equations. In this work, we focus on electric dipole excitations in spherical molybdenum isotopes, particularly 96 Mo, employing fully consistent Hartree-Fock-Bogoliubov (HFB) and Quasiparticle Random Phase Approximation (QRPA) methods. We analyze the dipole strength near the neutron separation energy, which represents the threshold for neutron capture processes, and examine the isospin characteristics of PDR states through transition density calculations. Examination of proton and neutron transition densities reveals distinctive features of each dipole state, indicating their isoscalar and isovector nature. We observe that the primary component in the enhanced low-energy region exhibits isovector character. The PDR displays a mixture of isoscalar and isovector nature, distinguishing it from the isovector giant dipole resonance (IVGDR). These findings lay the groundwork for future investigations into the role of transition densities in reaction models and for their application to inelastic scattering calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Deconvolution of dynamic heterogeneity in protein structure

Heterogeneity is intrinsic to the dynamic process of a chemical reaction. As reactants are converted to products via intermediates, the nature and extent of heterogeneity vary temporally throughout the duration of the reaction and spatially across the molecular ensemble. The goal of many biophysical techniques, including crystallography and spectroscopy, is to establish a reaction trajectory that follows an experimentally provoked dynamic process. It is essential to properly analyze and resolve heterogeneity inevitably embedded in experimental datasets. We have developed a deconvolution technique based on singular value decomposition (SVD), which we have rigorously practiced in diverse research projects. In this review, we recapitulate the motivation and challenges in addressing the heterogeneity problem and lay out the mathematical foundation of our methodology that enables isolation of chemically sensible structural signals. We also present a few case studies to demonstrate the concept and outcome of the SVD-based deconvolution. Finally, we highlight a few recent studies with mechanistic insights made possible by heterogeneity deconvolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Integrated edge-to-exascale workflow for real-time steering in neutron scattering experiments

We introduce a computational framework that integrates artificial intelligence (AI), machine learning, and high-performance computing to enable real-time steering of neutron scattering experiments using an edge-to-exascale workflow. Focusing on time-of-flight neutron event data at the Spallation Neutron Source, our approach combines temporal processing of four-dimensional neutron event data with predictive modeling for multidimensional crystallography. At the core of this workflow is the Temporal Fusion Transformer model, which provides voxel-level precision in predicting 3D neutron scattering patterns. The system incorporates edge computing for rapid data preprocessing and exascale computing via the Frontier supercomputer for large-scale AI model training, enabling adaptive, data-driven decisions during experiments. This framework optimizes neutron beam time, improves experimental accuracy, and lays the foundation for automation in neutron scattering. Although real-time experiment steering is still in the proof-of-concept stage, the demonstrated potential of this system offers a substantial reduction in data processing time from hours to minutes via distributed training, and significant improvements in model accuracy, setting the stage for widespread adoption across neutron scattering facilities and more efficient exploration of complex material systems.

97 MATHEMATICS AND COMPUTING↗

Reconstruction of the interatomic forces from dynamic scanning transmission electron microscopy data

We explore the possibility for reconstruction of the generative physical models describing interactions between atomic units in solids from observational electron microscopy data. In this work, scanning transmission electron microscopy (STEM) is used to observe the dynamic motion of Si atoms at the edge of monolayer graphene under continuous electron beam illumination. The resulting time-lapsed STEM images represent the snapshots of observed chemical states of the system. We use two approaches: potential of mean force calculation using a radial distribution function and a direct fitting of the graphene–Si interatomic pairwise potentials with force matching, to reconstruct the force fields in the materials. These studies lay the foundation for quantitative analysis of materials energetics from STEM data through the sampling of the metastable states in the chemical space of the system.

42 ENGINEERING↗

On the proper derivation of the Floquet-based quantum classical Liouville equation and surface hopping describing a molecule or material subject to an external field

We investigate different approaches to derive the proper Floquet-based quantum–classical Liouville equation (F-QCLE) for laser-driven electron-nuclear dynamics. The first approach projects the operator form of the standard QCLE onto the diabatic Floquet basis and then transforms to the adiabatic representation. The second approach directly projects the QCLE onto the Floquet adiabatic basis. Both approaches yield a form that is similar to the usual QCLE with two modifications: (1) The electronic degrees of freedom are expanded to infinite dimension and (2) the nuclear motion follows Floquet quasi-energy surfaces. However, the second approach includes an additional cross derivative force due to the dual dependence on time and nuclear motion of the Floquet adiabatic states. Our analysis and numerical tests indicate that this cross derivative force is a fictitious artifact, suggesting that one cannot safely exchange the order of Floquet state projection with adiabatic transformation. Our results are in accord with similar findings by Izmaylov et al., [J. Chem. Phys. 140, 084104 (2014)] who found that transforming to the adiabatic representation must always be the last operation applied, although now we have extended this result to a time-dependent Hamiltonian. Finally, this paper and the proper derivation of the F-QCLE should lay the basis for further improvements of Floquet surface hopping.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗