Accurate Nonempirical Range-Separated Hybrid van der Waals Density Functional for Complex Molecular Problems, Solids, and Surfaces
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Abstract The complex interactions among soil, vegetation, and site hydrologic conditions driven by precipitation and tidal cycles control the biogeochemical transformations and bi‐directional exchange of carbon and nutrients across the terrestrial–aquatic interfaces (TAIs) in coastal regions. This study uses a highly mechanistic model, Advanced Terrestrial Simulator (ATS)‐PFLOTRAN, to explore how these interactions affect exchanges of materials and carbon and nitrogen cycling. We used a transect in the Chesapeake Bay region that spans zones of open water, coastal wetland, transition, and upland forest. We designed several simulation scenarios to parse the effects of the individual controlling factors and the sensitivity of carbon cycling to reaction rate parameters derived from laboratory experiments. Our simulations reveal an active zone for carbon cycling under the transition zones between the wetland and the upland. Evapotranspiration is found to enhance the exchange fluxes between the surface and subsurface domains, resulting in a higher dissolved oxygen concentration in the TAIs. The transport of organic carbon derived from plant leaves and roots provide an additional source of organic carbon needed for the aerobic respiration and denitrification processes in the TAIs. The variability in reaction rate parameters associated with microbial activities is also found to play a dominant role in controlling the heterogeneity and dynamics of the simulated redox conditions. This modeling‐focused exploratory study enabled us to better understand the complex interactions among soil, water and microbes that govern the hydro‐biogeochemical processes at the TAIs, which is an important step toward representing coastal ecosystems in larger‐scale Earth system models.
Atomic disorder can strongly influence material properties such as charge transport, optical response, and catalytic activity. However, efficiently modeling these disorder effects remains challenging for first-principles methods due to the cost of sampling large configurational spaces and computing complex physical quantities. Recent advances of machine learning techniques, particularly graph neural networks (GNNs), has enabled the efficient and accurate predictions of complex material properties, offering promising tools for studying disordered systems. In this work, we present a general machine-learning-assisted computational framework that integrates equivariant GNNs with Monte Carlo simulations to compute the thermodynamic and ensemble-averaged functional properties of disordered materials. Using the surface-termination-disordered MXene monolayer Ti 3 C 2 T 2–x as a representative system, we find that electrical conductivity exhibits an emergent peak near the order–disorder phase transition temperature due to the interplay between electron scattering and doping. In contrast, optical conductivity remains largely insensitive to local atomic disorder and reflects the global surface chemical composition. These results highlight the role of atomic disorder in affecting material properties and demonstrate the potential of our approach for statistically modeling disorder effects in a wide range of materials such as high-entropy alloys and spin liquids.
It has long been conjectured that the large N deconfinement phase transition of $\mathcal{N}$ = 4 SU(N) super-Yang-Mills corresponds via AdS/CFT to the Hawking-Page transition in which black holes dominate the thermal ensemble, and quantitative evidence of this has come through the recent matching of the superconformal index of $\frac{1}{16}$-BPS states to the supersymmetric black hole entropy. Here we introduce the half-BPS Gukov-Witten surface defect as a probe of the superconformal index, which also serves as an order parameter for the deconfinement transition. This can be studied directly in field theory as a modification of the usual unitary matrix model or in the dual description as a D3-brane probe in the background of a (complex) supersymmetric black hole. Using a saddle point approximation, we determine our defect index in the large N limit as a simple function of the chemical potentials and show independently that it is reproduced by the renormalized action of the brane in the black hole background. Along the way, we also comment on the Cardy limit and the thermodynamics of the D3-brane in the generalized ensemble. The defect index sharply distinguishes between the confining and the deconfining phases of the gauge theory and thus is a supersymmetric non-perturbative order parameter for these large N phase transitions which deserves further investigation. Finally, our work provides an example where the properties of a black hole coupled to an external system can be analyzed precisely.
Nanodiamonds (ND) hosting negatively charged nitrogen-vacancy (NV-) color centers have received attention for applications in magnetic field, electric field, chemical, and bio-sensing. The versatility of these probes is their excellent room-temperature optical and spin properties, along with their small size, functionalized surfaces and resistance to bleaching, making them ideal as nanoscopic sensors in picoliter volumes (e.g. single cells, but also microcompartments and aerosols). For quantitative ND-NV- sensing of paramagnetic analytes in such contexts, however, there remains an incomplete understanding of how factors related to the aqueous phase environment control detection efficiency. To address this, optically detected magnetic resonance (ODMR) is measured in bulk macroscale solutions and single levitated microdroplets as a function of Gd+3 concentration (340 nM to 1.5 mM), nanodiamond size, pH, competitor ions, and ligands. The ODMR response to [Gd+3] is found to be nonlinear, and pH, ND and sample volume dependent; indicating the detection of Gd+3 requires efficient adsorption of the analyte to the diamond surface. Langmuir adsorption isotherms embedded in a quantitative photophysical model links the ODMR response to adsorption thermodynamics of Gd+3. The equilibrium constant for Gd+3 adsorption to a carboxylated ND surface is determined to be (1 ± 0.5) x 105 M-1 corresponding to a free energy of adsorption of (-28 ± 1) kJ mol-1. These results provide general insight into how complex aqueous and microscale environments impact nanodiamond based quantum sensing modalities, and portend their application as quantitative chemical sensors in microenvironments.
In a first-order phase transition, critical nucleus size governs nucleation kinetics, but the direct experimental test of the theory and determination of the critical nucleation size have been achieved only recently in the case of ice formation in supercooled water. The widely known metal-insulator phase transition (MIT) in strongly correlated VO 2 is a first-order electronic phase transition coupled with a solid-solid structural transformation. It is unclear whether classical nucleation theory applies in such a complex case. Here we directly measure the critical nucleus size of the MIT by introducing size-controlled nanoscale nucleation seeds with focused ion irradiation at the surface of a deeply supercooled metal phase of VO 2 . The results compare favorably with classical nucleation theory and are further explained by phase-field modeling. This Letter validates the application of classical nucleation theory as a parametrizable model to describe phase transitions of strongly correlated electron materials.
Building energy simulation is a critical tool for developing and testing advanced control strategies, such as Reinforcement Learning (RL), to provide demand flexibility and affordable energy costs. The recently introduced Smart Buildings Control Suite (sbsim) provides a lightweight, scalable, and data-calibrated simulation environment based on a 2D finite-difference model. However, the initial model primarily focused on conductive and convective heat transfer, neglecting the significant impact of long-wave radiative heat exchange between interior surfaces. This paper presents a significant extension to the sbsim framework by incorporating a physically-grounded model for interior radiative heat transfer. Our primary contribution is the development and integration of a fully tensorized radiative heat transfer module, which preserves the computational efficiency and scalability of the original simulator. This was achieved by developing a pipeline for view factor calculation, including an algorithm to identify directly seeing surfaces within complex floor plans, and formulating the net radiation equations for efficient execution on modern hardware accelerators. We validate the numerical accuracy of our tensorized implementation by comparing its results against a traditional iterative approach, demonstrating identical outcomes. This enhancement increases the physical fidelity of sbsim, enabling more accurate training of RL agents for building energy optimization.
With the highest albedo of the land surface, snow plays a vital role in Earth's surface energy budget and water cycle. Snow albedo is primarily controlled by snow grain properties (e.g., size and shape) and light-absorbing particles (LAPs) such as black carbon (BC) and dust. The mixing state of LAPs in snow also has impacts on LAP-induced snow albedo reduction and surface radiative forcing (RF). However, most land surface models assume that snow grain shape is spherical and LAPs are externally mixed with the snow grains. This study improves the snow radiative transfer model in the Energy Exascale Earth System Model version 2.0 (E3SM v2.0) Land Model (ELM v2.0) by considering non-spherical snow grain shapes (i.e., spheroid, hexagonal plate, and Koch snowflake) and internal mixing of dust–snow, and it systematically evaluates the impacts on the surface energy budget and water cycle over the Tibetan Plateau (TP). A series of ELM simulations with different treatments of snow grain shape, mixing state of BC–snow and dust–snow, and sub-grid topographic effects (TOP) on solar radiation are performed. Compared with two remote sensing snow products derived from the Moderate Resolution Imaging Spectroradiometer, the control ELM simulation (ELM_Control) with the default configurations of spherical snow grain shape, internal mixing of BC–snow, external mixing of dust–snow, and without TOP as well as the ELM simulation with new model features (ELM_New) can both capture the overall snow distribution reasonably. Additionally, ELM_New overall shows smaller biases in snow cover fraction than ELM_Control in spring when snowmelt is important for water management. The estimated LAP-induced RF in ELM_New ranges from 0 to 19.3 W m -2 with the area-weighted average value of 1.5 W m -2 that is comparable to the reported values in existing studies. The Koch snowflake shape, among other non-spherical shapes, shows the largest difference from the spherical shape in spring when snow processes related to the surface energy budget and water cycle have high importance. The impacts of the mixing state of LAP in snow are smaller than the shape effects and depend on snow grain shape. Compared to external mixing, internal mixing of LAP–snow can lead to larger snow albedo reduction and snowmelt, which further affect the surface energy budget and water cycle. The individual contributions of non-spherical snow shape, mixing state of LAP–snow, and local topography impacts on the snow and surface fluxes have different signs and magnitudes, and their combined effects may be negative or positive due to complex and nonlinear interactions among the factors. Overall, the changes in net solar radiation in spring due to individual and combined effects range from -28.6 to 16.9 W m -2 and -29.7 to 12.2 W m -2 , respectively. This study advances understanding of the role of snow grain shape and mixing state of LAP–snow in land surface processes and offers guidance for improving snow simulations and RF estimates in Earth system models under climate change.
Abstract In multi‐mineral fractured rocks, the altered porous layer on the fracture surface resulting from preferential dissolution of the fast‐reacting minerals can have profound impacts on subsequent chemical‐physical alteration of the fractures. This study adopts the micro‐continuum approach to provide further understanding of reactive transport processes in the altered layer (AL), and mass exchanges with the bordering matrix and fracture. The modeling framework couples the Darcy‐Brinkman‐Stokes (DBS) solver in COMSOL Multiphysics and the geochemical modeling capability of CrunchFlow. Three‐dimensional steady state simulations with systematically varied chemical‐physical parameters of the AL were performed to examine the impacts of individual factors and processes. Our simulation results confirm previous observations that dissolution of the fast‐reacting mineral (i.e., calcite) is largely controlled by diffusion across the AL. We also show that dissolution of the slow‐reacting mineral (i.e., dolomite), which controls AL development and fracture enlargement, increases with surface area and has a complex dependence on different local rate‐limiting processes. In particular, advection can result in evident spatial variations in the local dissolution rates of dolomite, although it does not affect the bulk chemistry significantly. The difference in the spatial patterns between simulations with and without advection in the AL is more noticeable in the locations with smaller apertures, with up to 20% difference in local reaction rates. Therefore, it is important to include a full depiction of advection, diffusion, and reactions for accurately capturing local dynamics that control long‐term fracture evolution.
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.
Understanding the behaviour of matter under conditions of extreme temperature, pressure, density and electromagnetic fields has profound effects on our understanding of cosmologic objects and the formation of the universe. Lacking direct access to such objects, our interpretation of observed data mainly relies on theoretical models. However, such models, which need to encompass nuclear physics, atomic physics and plasma physics over a huge dynamic range in the dimensions of energy and time, can only provide reliable information if we can benchmark them to experiments under well-defined laboratory conditions. Due to the plethora of effects occurring in this kind of highly excited matter, characterizing isolated dynamics or obtaining direct insight remains challenging. High-density plasmas are turbulent and opaque for radiation below the plasma frequency and allow only near-surface insight into ionization processes with visible wavelengths. Here, the output of a high-harmonic seeded laser-plasma amplifier using eight-fold ionized krypton as the gain medium operating at a 32.8 nm wavelength is ptychographically imaged. A complex-valued wavefront is observed in the extreme ultraviolet (XUV) beam with high resolution. Ab initio spatio-temporal Maxwell–Bloch simulations show excellent agreement with the experimental observations, revealing overionization of krypton in the plasma channel due to nonlinear laser-plasma interactions, successfully validating this four-dimensional multiscale model. This constitutes the first experimental observation of the laser ion abundance reshaping a laser-plasma amplifier. The presented approach shows the possibility of directly modelling light-plasma interactions in extreme conditions, such as those present during the early times of the universe, with direct experimental verification.
Solutions for improving fast charging of lithium‐ion batteries have largely focused on alleviating through‐plane lithiation gradients while little is understood about in‐plane heterogeneities and how to resolve them. Herein, high‐speed synchrotron X‐ray diffraction (XRD) resolves graphite lithiation spatially and temporally during 6 C charging and 2 C discharging. At every point during operation, considerable differences in the state of lithiation across the pouch cell are present. Some regions are more responsive to operation than others, reaching full lithiation early during charge and full delithiation during discharge. Other regions within the cell never fully delithiate during discharge, despite a prolonged voltage hold at 2.8 V. Using time‐resolved XRD data, the calculated local current density (mA cm −2 ) at the graphite surface shows an unexpected occurrence of local inverted current densities where regions of graphite are observed to delithiate during charging and lithiate during discharging. A pseudo‐3D model is developed for the graphite electrode with spatially varying microstructural tortuosity to show how microstructural heterogeneity could influence spatial charge dynamics. The model could not predict the complex in‐plane charge behavior observed within the cell. Consequently physics‐based charging protocols based on homogeneous electrode assumptions may underestimate the local variations in charge dynamics and occurrence of lithium plating.
Large format additive manufacturing (LFAM) is an advanced 3D printing technique that efficiently fabricates large-scale components through a layer-by-layer extrusion and deposition process. Accurate surface layer temperature monitoring is essential to prevent manufacturing failures and ensure final product quality. Traditional physics-based offline approaches for simulating thermal behavior are often inefficient and complex, posing challenges on real-time, in-situ monitoring. Here, to address this, we propose a data-driven hybrid CNN-LSTM model to predict sequential thermal images of arbitrary length using real-time infrared thermal imaging. In this approach, a Convolutional Neural Networks (CNN) is trained offline to capture spatial features, reduce dimensional complexity, and enhance time efficiency, while a stacked Long Short-Term Memory (LSTM) is applied online to capture temporal information for improved prediction of future thermal behavior in subsequent printing layers. Model performance is evaluated using MSE, SSIM, and PSNR metrics and is benchmarked against stacked LSTM and convolutional LSTM models, demonstrating superior accuracy and applicability. Additionally, to mitigate noise from moving extruders and gantry backgrounds in thermal images, a fine-tuned semantic segmentation model is implemented offline to extract printing geometry, enabling precise temperature tracking along the tool path for further thermal analysis. The frameworks developed in this study significantly advance temperature monitoring, thermal analysis, and in-situ manufacturing control for LFAM, bridging the gap between theoretical modeling and practical application.
Classical molecular dynamics (MD) simulations represent a very popular and powerful tool for materials modeling and design. The predictive power of MD hinges on the ability of the interatomic potential to capture the underlying physics and chemistry. There have been decades of seminal work on developing interatomic potentials, albeit with a focus predominantly on capturing the properties of bulk materials. Such physics-based models, while extensively deployed for predicting the dynamics and properties of nanoscale systems over the past two decades, tend to perform poorly in predicting nanoscale potential energy surfaces (PESs) when compared to high-fidelity first-principles calculations. These limitations stem from the lack of flexibility in such models, which rely on a predefined functional form. Machine learning (ML) models and approaches have emerged as a viable alternative to capture the diverse size-dependent cluster geometries, nanoscale dynamics, and the complex nanoscale PESs, without sacrificing the bulk properties. Here, in this study, we introduce an ML workflow that combines transfer and active learning strategies to develop high-dimensional neural networks (NNs) for capturing the cluster and bulk properties for several different transition metals with applications in catalysis, microelectronics, and energy storage, to name a few. Our NN first learns the bulk PES from the high-quality physics-based models in literature and subsequently augments this learning via retraining with a higher-fidelity first-principles training data set to concurrently capture both the nanoscale and bulk PES. Our workflow departs from status-quo in its ability to learn from a sparsely sampled data set that nonetheless covers a diverse range of cluster configurations from near-equilibrium to highly nonequilibrium as well as learning strategies that iteratively improve the fingerprinting depending on model fidelity. All the developed models are rigorously tested against an extensive first-principles data set of energies and forces of cluster configurations as well as several properties of bulk configurations for 10 different transition metals. Our approach is material agnostic and provides a methodology to transfer and build upon the learnings from decades of seminal work in molecular simulations on to a new generation of ML-trained potentials to accelerate materials discovery and design.
Abstract Understanding the complex interrelationships between wildfire and its environmental and anthropogenic controls is crucial for wildfire modeling and management. Although machine learning (ML) models have yielded significant improvements in wildfire predictions, their limited interpretability has been an obstacle for their use in advancing understanding of wildfires. This study builds an ML model incorporating predictors of local meteorology, land‐surface characteristics, and socioeconomic variables to predict monthly burned area at grid cells of 0.25° × 0.25° resolution over the contiguous United States. Besides these predictors, we construct and include predictors representing the large‐scale circulation patterns conducive to wildfires, which largely improves the temporal correlations in several regions by 14%–44%. The Shapley additive explanation is introduced to quantify the contributions of the predictors to burned area. Results show a key role of longitude and latitude in delineating fire regimes with different temporal patterns of burned area. The model captures the physical relationship between burned area and vapor pressure deficit, relative humidity (RH), and energy release component (ERC), in agreement with the prior findings. Aggregating the contribution of predictor variables of all the grids by region, analyses show that ERC is the major contributor accounting for 14%–27% to large burned areas in the western US. In contrast, there is no leading factor contributing to large burned areas in the eastern US, although large‐scale circulation patterns featuring less active upper‐level ridge‐trough and low RH two months earlier in winter contribute relatively more to large burned areas in spring in the southeastern US.
The Fast All-sky Radiation Model for Solar applications (FARMS) is used to compute cloudy irradiance. Radiative transfer (RT) models simulating broadband solar radiation have been widely used by atmospheric scientists to model solar resources for various energy applications such as operational forecasting. Due to the complexity of solving the RT equation, the computation under cloudy conditions can be extremely time consuming though many approximations (e.g. two-stream approach and delta-M truncation scheme) have been utilized. Thus, a more efficient RT model is crucial for model developers as a new option for approximating solar radiation at the land surface with minimal loss of accuracy. We have developed a fast all-sky radiation model for solar applications (FARMS) using the simplified clear-sky RT model, REST2, and simulated cloud transmittances and reflectances from the Rapid Radiation Transfer Model (RRTM) with a sixteen-stream Discrete Ordinates Radiative Transfer (DISORT). Simulated lookup tables (LUTs) of cloud transmittances and reflectances were created by varying cloud optical thicknesses, cloud particle sizes, and solar zenith angles. Equations with optimized parameters were fitted to the cloud transmittances and reflectances to develop the model. Using this model the all-sky solar irradiance at the land surface can be computed rapidly by combining REST2 with the cloud transmittances and reflectances. This new RT model is more than 1000 times faster than those currently utilized in solar resource assessment and forecasting since it does not explicitly solve the RT equation for each individual cloud condition. Our results indicate the accuracy of the fast radiative transfer model is comparable to or better than two-stream approximation in term of computing cloud transmittance and solar radiation.
Campylobacter jejuni CsrA is an mRNA-binding, post-transcriptional regulator that controls many metabolic- and virulence-related characteristics of this important pathogen. In contrast to E. coli CsrA, whose activity is modulated by binding to small non-coding RNAs (sRNAs), C. jejuni CsrA activity is controlled by binding to the CsrA antagonist FliW. In this study, we identified the FliW binding site on CsrA. Deletion of the C-terminus of C. jejuni CsrA, which is extended relative to sRNA-binding CsrA proteins, abrogated FliW binding. Bacterial two-hybrid experiments were used to assess the interaction of FliW with wild-type CsrA and mutants thereof, in which every amino acid was individually mutated. Two CsrA mutations (V51A and N55A) resulted in a significant decrease in FliW binding. The V51A and N55A mutants also showed a decrease in CsrA-FliW complex formation, as assessed by size-exclusion chromatography and surface plasmon resonance. These residues were highly conserved in bacterial species containing CsrA orthologs whose activities are predicted to be regulated by FliW. The location of FliW binding was immediately adjacent to the two RNA-binding sites of the CsrA homodimer, suggesting the model that FliW binding to CsrA modulates its ability to bind to its mRNA targets either by steric hindrance, electrostatic repulsion, or by altering the overall structure of the RNA-binding sites.
The Fast All-sky Radiation Model for Solar applications (FARMS) is used to compute cloudy irradiance. Radiative transfer (RT) models simulating broadband solar radiation have been widely used by atmospheric scientists to model solar resources for various energy applications such as operational forecasting. Due to the complexity of solving the RT equation, the computation under cloudy conditions can be extremely time consuming though many approximations (e.g. two-stream approach and delta-M truncation scheme) have been utilized. Thus, a more efficient RT model is crucial for model developers as a new option for approximating solar radiation at the land surface with minimal loss of accuracy. We have developed a fast all-sky radiation model for solar applications (FARMS) using the simplified clear-sky RT model, REST2, and simulated cloud transmittances and reflectances from the Rapid Radiation Transfer Model (RRTM) with a sixteen-stream Discrete Ordinates Radiative Transfer (DISORT). Simulated lookup tables (LUTs) of cloud transmittances and reflectances were created by varying cloud optical thicknesses, cloud particle sizes, and solar zenith angles. Equations with optimized parameters were fitted to the cloud transmittances and reflectances to develop the model. Using this model the all-sky solar irradiance at the land surface can be computed rapidly by combining REST2 with the cloud transmittances and reflectances. This new RT model is more than 1000 times faster than those currently utilized in solar resource assessment and forecasting since it does not explicitly solve the RT equation for each individual cloud condition. Our results indicate the accuracy of the fast radiative transfer model is comparable to or better than two-stream approximation in term of computing cloud transmittance and solar radiation.