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At least 163 records · Page 9

Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes

Protein–protein interactions play a key role in mediating numerous biological functions, with more than half the proteins in living organisms existing as either homo- or hetero-oligomeric assemblies. Protein subunits that form oligomers minimize the free energy of the complex, but exhaustive computational search-based docking methods have not comprehensively addressed the challenge of distinguishing a natively bound complex from non-native forms. Current protein docking approaches address this problem by sampling multiple binding modes in proteins and scoring each mode, with the lowest-energy (or highest scoring) binding mode being regarded as a near-native complex. However, high-scoring modes often match poorly with the true bound form, suggesting a need for improvement of the scoring function. Here in this study, we propose a scoring function, KFC-E, that accounts for both conservation and coevolution of putative binding hotspot residues at protein–protein interfaces. We tested KFC-E on four benchmark sets of unbound examples and two benchmark sets of bound examples, with the results demonstrating a clear improvement over scores that examine conservation and coevolution across the entire interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data-driven emulation of modal aerosol microphysics via neural operator-based modeling

The complexity and the small characteristic scales of aerosol microphysical processes pose a big challenge for accurate and efficient Earth system simulations at regional and global scales. In this work, we construct and evaluate a surrogate model: the aerosol deep operator network (ADON), a physics-inspired dual-net architecture for emulating the aerosol microphysics parameterization suite in the version 2 of the Energy Earth System Model (E3SMv2). The current version of the surrogate model is trained on a dataset comprising 9.8 million samples obtained from a global E3SMv2 simulation with the horizontal resolution of about one degree under cloud-free conditions. Incorporating domain spatial and temporal coordinates, as well as principle components extracted from training data, the dual-net surrogate model effectively captures the intricate representations of aerosol and the relationship with atmospheric state variables, achieving an R-squared score over $$95.7\%$$ for all the lognormal aerosol modes in the extrapolated regime. The validated model provides feature importance of input variables and their impact on the predictive capacity of the surrogate model in relation to the E3SM. The computational cost of online inference time deployed on CPUs and GPUs with lower precisions highlights ADON’s efficiency and potential in robust predictive modeling for large-scale Earth system computations.

Bai, Zhe↗

A Molecular View of Methane Activation on Ni(111) through Enhanced Sampling and Machine Learning

A combination of machine learned interatomic potentials (MLIPs) and enhanced sampling simulations is used to investigate the activation of methane on a Ni(111) surface. The work entails the development and iterative refinement of MLIPs, initially trained on a dataset constructed via ab initio molecular dynamics (AIMD) simulations, supplemented by adaptive biasing forces, to enrich the sampling of catalytically relevant configurations. Our results reveal that by incorporating collective variables that capture the behavior of the reactant molecule, as well as additional frames that describe the dynamic response of the catalytic surface, it is possible to enhance considerably the accuracy of predicted energies and forces. By employing enhanced sampling schemes in the refinement of the MLIP, we systematically explore the potential energy surface, leading to a refined MLIP capable of predicting DFT-level energies and forces and replicating key geometric characteristics of the catalytic system. The resulting free energy landscapes at several temperatures provide a detailed view of the thermodynamics and dynamics of methane activation. Specifically, as methane approaches and dissociates on the catalytic surface, the process involves the dynamic interplay of CH 4 and the Ni catalyst that includes both enthalpic and entropic contributions. The progression towards the transition state involves an CH 4 moiety that is increasingly restrained in its ability to rotate or translate, while the stage following the transition state is characterized by a notable rise of the Ni atom that interacts with the cleaved C–H bond. Furthermore, this leads to an increase in the mobility of the adsorbed species, a feature that becomes more pronounced at higher temperatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dark Energy Survey Year 3 results: Cosmological constraints from galaxy clustering and galaxy-galaxy lensing using the MagLim lens sample

The cosmological information extracted from photometric surveys is most robust when multiple probes of the large scale structure of the Universe are used. Two of the most sensitive probes are the clustering of galaxies and the tangential shear of background galaxy shapes produced by those foreground galaxies, so-called galaxy-galaxy lensing. Combining the measurements of these two two-point functions leads to cosmological constraints that are independent of the way galaxies trace matter (the galaxy bias factor). The optimal choice of foreground, or lens, galaxies is governed by the joint, but conflicting requirements to obtain accurate redshift information and large statistics. We present cosmological results from the full 5000 deg 2 of the Dark Energy Survey’s first three years of observations (Y3) combining those two-point functions, using for the first time a magnitude-limited lens sample (MagLim) of 11 million galaxies, especially selected to optimize such combination, and 100 million background shapes. We consider two flat cosmological models, the Standard Model with dark energy and cold dark matter ( Λ CDM ) a variation with a free parameter for the dark energy equation of state ( w CDM ). Both models are marginalized over 25 astrophysical and systematic nuisance parameters. In Λ CDM we obtain for the matter density Ω m = 0.320 - 0.034 + 0.041 and for the clustering amplitude S 8 ≡ σ 8 ( Ω m / 0.3 ) 0.5 = 0.778 - 0.031 + 0.037 , at 68% C.L. The latter is only 1 σ smaller than the prediction in this model informed by measurements of the cosmic microwave background by the Planck satellite. In w CDM we find Ω m = 0.32 - 0.046 + 0.044 , S 8 = 0.777 - 0.051 + 0.049 and dark energy equation of state w = - 1.031 - 0.379 + 0.218 . We find that including smaller scales, while marginalizing over nonlinear galaxy bias, improves the constraining power in the Ω m - S 8 plane by 31% and in the Ω m - w plane by 41% while yielding consistent cosmological parameters from those in the linear bias case. These results are combined with those from cosmic shear in a companion paper to present full DES-Y3 constraints from the three two-point functions ( 3 × 2 pt ).

79 ASTRONOMY AND ASTROPHYSICS↗

Probing the self-ionization of liquid water with ab initio deep potential molecular dynamics

The chemical equilibrium between self-ionized and molecular water dictates the acid–base chemistry in aqueous solutions, yet understanding the microscopic mechanisms of water self-ionization remains experimentally and computationally challenging. Herein, Density Functional Theory (DFT)–based deep neural network (DNN) potentials are combined with enhanced sampling techniques and a global acid–base collective variable to perform extensive atomistic simulations of water self-ionization for model systems of increasing size. The explicit inclusion of long-range electrostatic interactions in the DNN potential is found to be crucial to accurately reproduce the DFT free energy profile of solvated water ion pairs in small (64 and 128 H 2 O) cells. The reversible work to separate the hydroxide and hydronium to a distance S is found to converge for simulation cells containing more than 500 H 2 O, and a distance of ∼ 8 Å is the threshold beyond which the work to further separate the two ions becomes approximately zero. The slow convergence of the potential of mean force with system size is related to a restructuring of water and an increase of the local order around the water ions. Calculation of the dissociation equilibrium constant illustrates the key role of long-range electrostatics and entropic effects in the water autoionization process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Maximizing Calendering Effects Through the Mechanical Pulverization of Co-Free Nickel-Rich Cathodes in Lithium-Ion Cells

Calendering is a technique used to maximize the volumetric energy density of battery electrodes. However, higher amounts of calendering result in increased tortuosity and particle cracking. We propose a novel packing structure of electrode particles to maximize calendering benefits while minimizing particle fracture. Cobalt-free layered oxide cathode LiNi0.92Mn0.04Al0.04O2 (NMA) particles are pulverized through ball-milling and coated with lithium phosphate. Pulverized and pristine NMA are fabricated into “bimodal” electrodes, whereas “unimodal” electrodes consist of only pristine NMA. Each electrode type was made into 30% porosity, 40% porosity, and uncalendered coin cell samples. X-ray diffraction suggests that the unimodal samples suffer from more particle fracture than the bimodal samples when calendered to the same porosity of 30%. Electrochemical impedance spectroscopy suggests that the bimodal electrodes exhibit lower surface film resistance. This is supported by enhanced capacity retention for the bimodal samples after 100 cycles.

25 ENERGY STORAGE↗

Uranium (VI) Adsorbate Structures on Portlandite [Ca(OH)2] Type Surfaces Determined by Computational Modelling and X-ray Absorption Spectroscopy

Portlandite [Ca(OH) 2 ] is a potentially dominant solid phase in the high pH fluids expected within the cementitious engineered barriers of Geological Disposal Facilities (GDF). This study combined X-ray Absorption Spectroscopy with computational modelling in order to provide atomic-scale data which improves our understanding of how a critically important radionuclide (U) will be adsorbed onto this phase under conditions relevant to a GDF environment. Such data are fundamental for predicting radionuclide mass transfer. Surface coordination chemistry and speciation of uranium with portlandite [Ca(OH) 2 ] under alkaline groundwater conditions (ca. pH 12) were determined by both in situ and ex situ grazing incidence extended X-ray absorption fine structure analysis (EXAFS) and by computational modelling at the atomic level. Free energies of sorption of aqueous uranyl hydroxides, [UO 2 (OH) n ] 2–n (n = 0–5) with the (001), (100) and (203) or (101) surfaces of portlandite are predicted from the potential of mean force using classical molecular umbrella sampling simulation methods and the structural interactions are further explored using fully periodic density functional theory computations. Although uranyl is predicted to only weakly adsorb to the (001) and (100) clean surfaces, there should be significantly stronger interactions with the (203/101) surface or at hydroxyl vacancies, both prevalent under groundwater conditions. The uranyl surface complex is typically found to include four equatorially coordinated hydroxyl ligands, forming an inner-sphere sorbate by direct interaction of a uranyl oxygen with surface calcium ions in both the (001) and (203/101) cases. In contrast, on the (100) surface, uranyl is sorbed with its axis more parallel to the surface plane. The EXAFS data are largely consistent with a surface structural layer or film similar to calcium uranate, but also show distinct uranyl characteristics, with the uranyl ion exhibiting the classic dioxygenyl oxygens at 1.8 Å and between four and five equatorial oxygen atoms at distances between 2.28 and 2.35 Å from the central U absorber. These experimental data are wholly consistent with the adsorbate configuration predicted by the computational models. These findings suggest that, under the strongly alkaline conditions of a cementitious backfill engineered barrier, there would be significant uptake of uranyl by portlandite to inhibit the mobility of U(VI) from the near field of a geological disposal facility.

36 MATERIALS SCIENCE↗

Data and scripts associated with “Moisture content modulates DOM thermodynamic regulation of oxygen consumption in drying streambed sediments”

This data package is associated with the publication “Moisture content modulates DOM thermodynamic regulation of oxygen consumption in drying streambed sediments” published in Scientific Reports (Garayburu-Caruso et al., 2026). The package contains processed data products and scripts used to quantify how drying and re-inundation of riverbed sediments influence dissolved organic matter (DOM) thermodynamic properties and their relationship with sediment oxygen (O₂) consumption across 33 stream sites in the contiguous United States. The data package contains DOM thermodynamic metrics (e.g., Gibbs free energy of carbon oxidation and thermodynamic efficiency), and O₂ consumption along with watershed-scale climate and land-cover metrics used as explanatory variables in the analyses. Underlying unprocessed and processed ultrahigh-resolution mass spectrometry data, oxygen consumption rates from laboratory moisture-manipulation experiments, within-sample environmental properties, sediment moisture content and contextual field measurements are archived separately at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/2428003 (Laan et al., 2024) and https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1923689 (Forbes et al.,2023). A preliminary version of this data package was published in February 2026 at the time of manuscript submission. It was updated in June 2026, at the time of manuscript acceptance, to include the finalized data and additional metadata (readme, data dictionary, and file level metadata). For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. At the top level, the data package is organized into five main folders: (1) Data, (2)Figures, (3) Map, (4) GAM_Reulsts, and (5) src. The Data folder contains analysis-ready tabular files with oxygen consumption rates, DOM thermodynamic properties by site and treatment, site-level environmental variables, watershed-scale metrics, and other derived variables referenced in the manuscript. The Figures folder contains static image files associated with the main text and supplemental figures, while the Map folder includes spatial data and map-layer files used to create the sampling-location map. The GAM results folder contains the results for each of the general additive model (GAM).The src folder contains R scripts used to perform data processing, statistical analyses (including clustering, generalized additive models, and threshold analysis), and figure generation. This data package is associated with a GitHub repository found at https://github.com/WHONDRS-Hub/ECA_DOM_Thermodynamics.

Dissolved organic matter↗

Adsorbate Partition Functions via Phase Space Integration: Quantifying the Effect of Translational Anharmonicity on Thermodynamic Properties

A new method for computing anharmonic thermophysical properties for adsorbates on metal surfaces is presented. Classical Monte Carlo phase space integration is performed to calculate the partition function for the motion of a hydrogen atom on Cu(111). Here, a minima-preserving neural network potential energy surface is used within the integration routine. Two different sampling schema for generating the training data are presented, and two different density functionals are used. The results are benchmarked against direct state counting results by using discrete variable representation. The phase space integration results are in excellent quantitative agreement with the benchmark results. Additionally, both the discrete variable representation and the phase space integration results confirm that the motion of H on Cu(111) is highly anharmonic. The results were applied to calculate the free energy of dissociative adsorption of H 2 and the resulting Langmuir isotherms at 400, 800, and 1200 K in a partial pressure range of 0–1 bar. It shows that the anharmonic effects lead to significantly higher predicted surface site fractions of hydrogen.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transient local secondary structure in the intrinsically disordered C‐term of the Albino3 insertase

Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light‐harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma‐exposed C‐terminus (Alb3‐Cterm) that is responsible for binding the LHC‐loaded transit complex before LHC membrane insertion. Alb3‐Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single‐molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site‐directed mutagenesis, trypsin digestion assays, and all‐atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3‐Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter‐residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3‐Cterm for the LHC‐loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3‐Oxa1‐YidC family of insertases.

Okoto, Patience S.↗

Simulations of activities, solubilities, transport properties, and nucleation rates for aqueous electrolyte solutions

This article reviews recent molecular simulation studies of "collective" properties of aqueous electrolyte solutions, specifically free energies and activity coefficients, solubilities, nucleation rates of crystals, and transport coefficients. These are important fundamental properties for biology and geoscience, but also relevant for many technological applications. Their determination from molecular-scale calculations requires large systems and long sampling times, as well as specialized sampling algorithms. As a result, such properties have not typically been taken into account during optimization of force field parameters; thus, they provide stringent tests for the transferability and range of applicability of proposed molecular models. There has been significant progress on simulation algorithms to enable the determination of these properties with good statistical uncertainties. Comparisons of simulation results to experimental data reveal deficiencies shared by many commonly used models. Moreover, there appear to exist specific tradeoffs within existing modeling frameworks, so that good prediction of some properties is linked to poor prediction for specific other properties. For example, non-polarizable models that utilize full charges on the ions generally fail to predict accurately both activity coefficients and solubilities; the concentration dependence of viscosity and diffusivity for these models is also incorrect. Scaled-charge models improve the dynamic properties and could also perform well for solubilities, but fail in the prediction of nucleation rates. Even models that do well at room temperature for some properties generally fail to capture their experimentally observed temperature dependence. Finally, the main conclusion from the present review is that qualitatively new physics will need to be incorporated in future models of electrolyte solutions to allow description of collective properties for broad ranges of concentrations, temperatures, and solvent conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Intrinsic spatial chirp of subcycle terahertz pulsed beams

Here, we present an analysis of spatial chirp in subcycle pulsed beams corroborated by spatiotemporal electro-optic sampling measurements of terahertz radiation. Modeling the subcycle pulsed beam as a superposition of monochromatic Gaussian beams, free-space propagation is shown to directly lead to lateral spatial chirp with the spectrum on-axis substantially bluer than the overall energy spectrum. The two-transverse + one-temporal dimensional profile of terahertz subcycle pulsed beams from organic crystals DSTMS and OH1 are measured and compared with observed spatiospectral correlations consistent with the model.

43 PARTICLE ACCELERATORS↗

Atomistic thermodynamics and kinetics of dicalcium silicate dissolution

Low-temperature cement manufacturing has garnered academic and industrial attention for its low environmental footprints. However, the sluggish hydration kinetics of the resultant cement affects their early-age strength development. This motivates fundamental studies to unravel the mechanistic picture of the dissolution process and discover science-informed pathways to accelerate hydration. Standard atomistic simulations seldomly exceed a microsecond making them impractical to study slow dissolution processes. We are using rare event sampling techniques, we provide the mechanistic picture of Ca 2+ ion dissolution from a kink site on the dicalcium silicate surface. The Ca 2+ ion dissolution is comprised of two sequential stages: breaking restraints from the kink sites to form a ledge adatom and detaching from the ledge/terrace adatom sites into the solution. The first and second stages feature free energy barriers of ~63 kJ/mol and ~ 29 kJ/mol respectively, making the first stage the rate-limiting step of the entire Ca 2+ dissolution kinetics. Using the reactive flux method, the rate and equilibrium constants for each reaction step are calculated, which yield the Ca 2+ ion activity of ~1.03 × 10 -5 . The diffusion calculations indicate that the surface effects lower the self-diffusion coefficient of Ca 2+ ions at the solid-water interface.

36 MATERIALS SCIENCE↗

Promoting the oxidative coupling of methanol and dimethylamine using group 1 alkali metals on palladium-gold nanoparticles

PdAu/SiO 2 catalysts were synthesized by strong electrostatic adsorption (SEA) and characterized by TEM, DRIFTS, XRD, XAS, and O 2 -TPD. The use of group 1 alkali salt solutions to control pH during SEA syntheses led to uptake of alkali metals observed reductions in the densities of terminal silanol groups of the SiO 2 support. In the absence of alkali metals, PdAu/SiO 2 catalyzes oxidative C-N bond formation between methanol and dimethylamine (DMA), yielding dimethylformamide (DMF) with ∼95 % carbon selectivity (CO 2 ∼5 %) at temperatures below 413 K. When Na, K, and Cs were present on the catalyst, methyl formate (MF) and tetramethylurea (TMU) were observed as additional products (combined ∼30 % carbon selectivity) while only TMU was detected for the Li-promoted catalyst. Total coupling product rate increased for promoted samples in the order Li < Na < Cs < K, and the apparent kinetics over the Cs-promoted catalyst were distinct from those over the alkali-free catalyst as the apparent reaction order with respect to DMA decreased and the apparent activation energy increased. Finally, this work demonstrates the sensitivity of oxidative coupling reactions to alkali metal promoters and the opportunity to achieve alkali promotion of metal catalysts during SEA synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electrofracturing of Shale at Elevated Pressure

Electrofracturing deeply buried shale formations could be used to increase reservoir permeability and improve reservoir production without requiring large volumes of freshwater. This paper describes a novel experimental system and initial test results to electrofracture shale under high confining pressures. Core-scale laboratory testing was performed on twelve rock samples recovered from a shale gas reservoir. Each sample was subjected to confining pressures of 20.7 MPa (3000 psi) or 58.6 MPa (8000 psi), representative of overburden pressures at depth. Samples were then subjected to application of high voltage until specimen fracture. The experiments produced deformed samples with multiple fracture types, both parallel and oblique to bedding planes. Electrofracturing increased permeabilities by up to nine orders of magnitude for extended time periods. Rock fracture and throughgoing fractures were demonstrated. Computed tomography images revealed the creation of fractures and tube/tunnel flow channels, which resisted closure under hydrostatic pressures up to 58.6 MPa. The breakdown energy and permeability changes in the sample were independent of applied confining pressure. The cumulative energy input required for fracture depended on applied confining pressure and sample length. The energy required to fracture samples up to 9 cm in length is generally more than 0.5 kJ/cm, but no greater than 1 kJ/cm. Our results show that electrofracture of shales under confining pressure is possible and could be a possible water-free mechanism for reservoir stimulation.

04 OIL SHALES AND TAR SANDS↗

The Completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: Cosmological Implications from two Decades of Spectroscopic Surveys at the Apache Point observatory

We present the cosmological implications from final measurements of clustering using galaxies, quasars, and Ly$\alpha$ forests from the completed Sloan Digital Sky Survey (SDSS) lineage of experiments in large-scale structure. These experiments, composed of data from SDSS, SDSS-II, BOSS, and eBOSS, offer independent measurements of baryon acoustic oscillation (BAO) measurements of angular-diameter distances and Hubble distances relative to the sound horizon, $r_d$, from eight different samples and six measurements of the growth rate parameter, $f\sigma_8$, from redshift-space distortions (RSD). This composite sample is the most constraining of its kind and allows us to perform a comprehensive assessment of the cosmological model after two decades of dedicated spectroscopic observation. We show that the BAO data alone are able to rule out dark-energy-free models at more than eight standard deviations in an extension to the flat, $\Lambda$CDM model that allows for curvature. When combined with Planck Cosmic Microwave Background (CMB) measurements of temperature and polarization the BAO data provide nearly an order of magnitude improvement on curvature constraints. The RSD measurements indicate a growth rate that is consistent with predictions from Planck primary data and with General Relativity. When combining the results of SDSS BAO and RSD with external data, all multiple-parameter extensions remain consistent with a $\Lambda$CDM model. Regardless of cosmological model, the precision on $\Omega_\Lambda$, $H_0$, and $\sigma_8$, remains at roughly 1\%, showing changes of less than 0.6\% in the central values between models. The inverse distance ladder measurement under a o$w_0w_a$CDM yields $H_0= 68.20 \pm 0.81 \, \rm km\, s^{-1} Mpc^{-1}$, remaining in tension with several direct determination methods. (abridged)

79 ASTRONOMY AND ASTROPHYSICS↗

Copper carbon composite wire with a uniform carbon dispersion made by friction extrusion

Copper-carbon composites are a group of materials with excellent mechanical, electrical, thermal, and tribological properties. However, bulk size copper-carbon composites made by the traditional manufacturing processes, like rolling or extrusion, fall short of reaching some of these properties predicted by theory or demonstrated only by samples at centimeter scale or smaller. The two main challenges to the successful scaling-up are: 1) to uniformly disperse carbon in the metal matrix; 2) to avoid degradation due to oxidation or reaction from overheating. In this work, we first demonstrate friction extrusion as a new method to make bulk-size void-free copper-carbon composite wires with homogenized carbon dispersion. Three different carbon varieties, graphite powder, graphene nanopowder, and carbon nanotubes, were added to the copper matrix with the concentration ranging from 0.5 wt% to 15 wt%. Special tooling, processing parameters, and procedures were developed, especially for high carbon content samples. Ten-fold reductions of both copper grain size and carbon particle size were achieved and attributed to the high shear deformation. Energy dispersive X-ray spectrometry indicates the carbon powder was refined to a sub-micron level and uniformly dispersed in the copper matrix. Compared with that of pure copper, the thermal capacity of the composite wire increases by 30 % while density reduces by 29 %.

Friction extrusion, Metal matrix composite, Graphe↗

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials

Silicon carbide (SiC) divacancies are attractive candidates for spin-defect qubits possessing long coherence times and optical addressability. The high activation barriers associated with SiC defect formation and motion pose challenges for their study by first-principles molecular dynamics. In this work, we develop and deploy machine learning interatomic potentials (MLIPs) to accelerate defect dynamics simulations while retaining ab initio accuracy. We employ an active learning strategy comprising symmetry-adapted collective variable discovery and enhanced sampling to compile configurationally diverse training data, calculation of energies and forces using density functional theory (DFT), and training of an E(3)-equivariant MLIP based on the Allegro model. Here, the trained MLIP reproduces DFT-level accuracy in defect transition activation free energy barriers, enables the efficient and stable simulation of multidefect 216-atom supercells, and permits an analysis of the temperature dependence of defect thermodynamic stability and formation/annihilation kinetics to propose an optimal annealing temperature to maximally stabilize VV divacancies.

Computer simulations↗