Studies of Mineral Nucleation and Growth Across Multiple Scales: Review of the Current State of Research Using the Example of Barite (BaSO 4 )
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides
Antibiotic resistance poses an immediate and growing threat to human health. Multidrug efflux pumps are promising targets for overcoming antibiotic resistance with small-molecule therapeutics. Previously, we identified a diaminoquinoline acrylamide, NSC-33353, as a potent inhibitor of the AcrAB–TolC efflux pump in Escherichia coli. This inhibitor potentiates the antibacterial activities of novobiocin and erythromycin upon binding to the membrane fusion protein AcrA. It is also a substrate for efflux and lacks appreciable intrinsic antibacterial activity of its own in wild-type cells. Here, we have modified the substituents of the cinnamoyl group of NSC-33353, giving rise to analogs that retain the ability to inhibit efflux, lost the features of the efflux substrates, and gained antibacterial activity in wild-type cells. The replacement of the cinnamoyl group with naphthyl isosteres generated compounds that lack antibacterial activity but are both excellent efflux pump inhibitors and substrates. Surprisingly, these inhibitors potentiate the antibacterial activity of novobiocin but not erythromycin. Surface plasmon resonance experiments and molecular docking suggest that the replacement of the cinnamoyl group with naphthyl shifts the affinity of the compounds away from AcrA to the AcrB transporter, making them better efflux substrates and changing their mechanism of inhibition. These results provide new insights into the duality of efflux substrate/inhibitor features in chemical scaffolds that will facilitate the development of new efflux pump inhibitors.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The Role of Premagmatic Rifting in Shaping a Volcanic Continental Margin: An Example From the Eastern North American Margin
Both magmatic and tectonic processes contribute to the formation of volcanic continental margins. Such margins are thought to undergo extension across a narrow zone of lithospheric thinning (~100 km). New observations based on existing and reprocessed data from the Eastern North American Margin contradict this hypothesis. With ~64,000 km of 2-D seismic data tied to 40 wells combined with published refraction, deep reflection, receiver function, and onshore drilling efforts, we quantified along-strike variations in the distribution of rift structures, magmatism, crustal thickness, and early post-rift sedimentation under the shelf of Baltimore Canyon Trough (BCT), Long Island Platform, and Georges Bank Basin (GBB). Results indicate that BCT is narrow (80–120 km) with a sharp basement hinge and few rift basins. The seaward dipping reflectors (SDR) there extend ~50 km seaward of the hinge line. In contrast, the GBB is wide (~200 km), has many syn-rift structures, and the SDR there extend ~200 km seaward of the hinge line. Early post-rift depocenters at the GBB coincide with thinner crust suggesting “uniform” thinning of the entire lithosphere. Models for the formation of volcanic margins do not explain the wide structure of the GBB. We argue that crustal thinning of the BCT was closely associated with late syn-rift magmatism, whereas the broad thinning of the GBB segment predated magmatism. Correlation of these variations to crustal terranes of different compositions suggests that the inherited rheology determined the premagmatic response of the lithosphere to extension.
58 GEOSCIENCES↗
The Role of Groundwater Withdrawals on River Regulation: Example From the Columbia River Basin
The Columbia River Basin (CRB) is heavily regulated by more than 250 dams on its river system while depending significantly on groundwater withdrawals in certain sub-basins. Neglecting groundwater withdrawals in hydrologic models of the basin could result in inaccurate predictions of its water budget and thus mislead water management decisions in the basin. This work aims to understand the impacts of groundwater pumping on the spatiotemporal patterns of modeling regulated streamflow in the CRB using a modified version of the Variable Infiltration Capacity (VIC) model integrated with a water management component that accounts for groundwater withdrawals, irrigation demands, and reservoir operation (VIC-GIRR). The VIC-GIRR simulations showed that considering additional groundwater withdrawals would alleviate the stress of irrigation water deficit in the Snake River Basin with an average reduction of 10 km 3 /year. Such a reduction in water deficit resulted in slight streamflow increase over the CRB with maximum increase up to 40% during dry period in certain locations. We also note that the implementation of groundwater withdrawal does not, however, improve the overall model performance in long-term averaged streamflow and storage predictions. Our results highlight the efforts needed to examine additional important processes in representing the interactions between water withdrawals and reservoir operations. Such efforts will aid in better simulation of multi-reservoir system and improve effectiveness for agricultural productivity, power generation, flood control, and navigation purposes.
54 ENVIRONMENTAL SCIENCES↗
Interplay Between Crustal‐Scale Thrusting, High Metamorphic Heating Rates, and the Development of Inverted Thermal‐Metamorphic Gradients: Numerical Models and Examples From the Caledonides of Northern Scotland
Abstract Understanding the processes that produce high prograde metamorphic heating rates and the development of inverted metamorphic sequences in collisional thrust belts remains a fundamental challenge for tectonics and metamorphic petrology. New 2D finite element models of crustal‐scale thrusts with variable slip rates (10, 20, 35, 50 km Myr −1 ) are used to examine how thrust sheet emplacement contributes to these processes. In the models, average prograde heating rates of 31–118 °C Myr −1 are observed in the footwall, with maximum transient heating rates of ∼167 °C Myr −1 occurring at the highest slip rate. Also, thrust sheet emplacement produces an inverted thermal gradient in the model footwall. At slip rates of 10 km Myr −1 , heating magnitudes >200 °C are observed >7 km structurally beneath the thrust plane. At slip rates of 20–50 km Myr −1 , models produce thermal penetration depths of 4–5 km for similar heating magnitudes. Petrologically determined heating rates for thrust footwalls in the Scandian orogenic wedge of northern Scotland mostly yield rates consistent with model results (10–230 °C Myr −1 ). The model‐derived magnitude of inverted thermal gradients is also similar to those indicated in texturally determined deformation temperature transects across the Scandian orogenic wedge (100 °C–180 °C). Combined, these results indicate that high heating rates can be produced by fault slip at typical plate velocities. Additionally, this implies that crustal‐scale thrusts are likely to produce inverted metamorphic sequences in most systems, provided that P‐T conditions during slip allow for metamorphic or recrystallization processes that would preserve evidence for such features.
Thigpen, J. Ryan↗
Selecting Appropriate Model Complexity: An Example of Tracer Inversion for Thermal Prediction in Enhanced Geothermal Systems
Abstract A major challenge in the inversion of subsurface parameters is the ill‐posedness issue caused by the inherent subsurface complexities and the generally spatially sparse data. Appropriate simplifications of inversion models are thus necessary to make the inversion process tractable and meanwhile preserve the predictive ability of the inversion results. In this study, we investigate the effect of model complexity on fracture aperture inversion and thermal performance prediction in a field‐scale EGS model. Principal component analysis was used to map the aperture field to a low‐dimensional latent space. The complexity of the inversion model was quantitatively represented by the percentage of total variance in the original aperture fields preserved by the latent space. Tracer, pressure and flow rate data were used to invert for fracture aperture through an ensemble‐based inversion method, and the inferred aperture field was used to predict thermal performance. With an over‐simplified aperture model, ensemble collapse occurred. The inverted aperture models failed to resolve necessary flow and transport features, leading to a biased thermal performance prediction. A complex aperture model involved excessive features and was prone to overinterpreting the inversion data. Both the tracer/pressure/flow rate data reproduction and thermal prediction showed significant uncertainties, making it difficult to properly estimate long‐term thermal performance. Fortunately, our results indicate that there exists an appropriate model complexity which can simultaneously match inversion data and predict thermal performance with an acceptable uncertainty. The quality of the fit of tracer data appears to be a useful indicator of such an appropriate model complexity.
15 GEOTHERMAL ENERGY↗
Machine-learned impurity level prediction for semiconductors: the example of Cd-based chalcogenides
The ability to predict the likelihood of impurity incorporation and their electronic energy levels in semiconductors is crucial for controlling its conductivity, and thus the semiconductor's performance in solar cells, photodiodes, and optoelectronics. The difficulty and expense of experimental and computational determination of impurity levels makes a data-driven machine learning approach appropriate. In this work, we show that a density functional theory-generated dataset of impurities in Cd-based chalcogenides CdTe, CdSe, and CdS can lead to accurate and generalizable predictive models of defect properties. By converting any semiconductor + impurity system into a set of numerical descriptors, regression models are developed for the impurity formation enthalpy and charge transition levels. These regression models can subsequently predict impurity properties in mixed anion CdX compounds (where X is a combination of Te, Se and S) fairly accurately, proving that although trained only on the end points, they are applicable to intermediate compositions. We make machine-learned predictions of the Fermi-level-dependent formation energies of hundreds of possible impurities in 5 chalcogenide compounds, and we suggest a list of impurities which can shift the equilibrium Fermi level in the semiconductor as determined by the dominant intrinsic defects. Machine learning predictions for the dominating impurities compare well with DFT predictions, revealing the power of machine-learned models in the quick screening of impurities likely to affect the optoelectronic behavior of semiconductors.
36 MATERIALS SCIENCE↗
Tuning the UV spectrum of PAHs by means of different N-doping types taking pyrene as paradigmatic example: categorization via valence bond theory and high-level computational approaches
Nitrogen doping leads to biradicloid character and subsequent UV red shift.
Shao, Xin↗
Modeling of surface mechanical behaviors of soft elastic solids: theory and examples
Surfaces of soft solids can have significant surface stress, extensional modulus and bending stiffness. Previous theoretical studies have usually examined cases in which both the surface stress and bending stiffness are constant, assuming small deformation. In this work we consider a general formulation in which the surface can support large deformation and carry both surface stresses and surface bending moments. We show that the large deformation theory can be reduced to the classical linear theory (Shuttleworth equation). We obtain exact solutions for problems of an inflated cylindrical shell and bending of a plate with a finite thickness. Our analysis illustrates the different manners in which surface stiffening and surface bending stabilize these structures. We discuss how the complex surface constitutive behaviors affect the stress field of the bulk. Our calculation provides insights into effects of strain-dependent surface stress and surface bending in the large deformation regime, and can be used as a model to implement surface finite elements to study large deformation of complex structures.
36 MATERIALS SCIENCE↗
14 examples of how LLMs can transform materials science and chemistry: a reflection on a large language model hackathon
We report the findings of a hackathon focused on exploring the diverse applications of large language models in molecular and materials science.
36 MATERIALS SCIENCE↗
Strategies to alleviate distortive phase transformations in Li-ion intercalation reactions: an example with vanadium pentoxide
This mini-review highlights recent materials design strategies to alleviate distortive phase transformations in vanadium pentoxide materials for energy storage applications and characterization methods.
Chemistry↗
Example of exponentially enhanced magnetic reconnection driven by a spatially bounded and laminar ideal flow
In laboratory and natural plasmas of practical interest, the spatial scale Δ d at which magnetic field lines lose distinguishability differs enormously from the scale a of magnetic reconnection across the field lines. In the solar corona, plasma resistivity gives a/Δ d ~ 10 12 , which is the magnetic Reynold number R m . The traditional resolution of the paradox of disparate scales is for the current density j associated with the reconnecting field Brec to be concentrated by a factor of Rm by the ideal evolution, so j ~ B rec /µ 0 Δ d . A second resolution is for the ideal evolution to increase the ratio of the maximum to minimum separation between pairs of arbitrarily chosen magnetic field lines, Δ max /Δ min , when calculated at various points in time. Reconnection becomes inevitable where Δ max /Δ min ~ R m . A simple model of the solar corona will be used for a numerical illustration that the natural rate of increase in time is linear for the current density but exponential for Δ max /Δ min . Reconnection occurs on a time scale and with a current density enhanced by only ln(a/Δ d ) from the ideal evolution time and from the current density B rec /µ 0 a. In both resolutions, once a sufficiently wide region, Δ r , has undergone reconnection, the magnetic field loses static force balance and evolves on an Alfv´enic time scale. The Alfv´enic evolution is intrinsically ideal but expands the region in which Δ max /Δ min is large.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Avoiding pitfalls in molecular simulation of vapor sorption: Example of propane and isobutane in metal–organic frameworks for adsorption cooling applications
This study introduces recommendations for conducting molecular simulations of vapor adsorption, with an emphasis on enhancing the accuracy, reproducibility, and comparability of results. The first aspect we address is consistency in the implementation of some details of typical molecular models, including tail corrections and cutoff distances, due to their significant influence on generated data. We highlight the importance of explicitly calculating the saturation pressures at relevant temperatures using methods such as Gibbs ensemble Monte Carlo simulations and illustrate some pitfalls in extrapolating saturation pressures using this method. For grand canonical Monte Carlo (GCMC) simulations, the input fugacity is usually calculated using an equation of state, which often requires the critical parameters of the fluid. We show the importance of using critical parameters derived from the simulation with the same model to ensure internal consistency between the simulated explicit adsorbate phase and the implicit bulk phase in GCMC. We show the advantages of presenting isotherms on a relative pressure scale to facilitate easier comparison among models and with experiment. Extending these guidelines to a practical case study, we evaluate the performance of various isoreticular metal–organic frameworks (MOFs) in adsorption cooling applications. This includes examining the advantages of using propane and isobutane as working fluids and identifying MOFs with a superior performance.
36 MATERIALS SCIENCE↗
An incomplete taxonomy of Bayesian models with examples from industrial statistics applications
Here, we consider a taxonomy of data types, structural components (including hierarchical levels), and stochastic components for developing Bayesian models for data analysis.
42 ENGINEERING↗
Beyond standard model particles in the atmospheric flux: a long-lived stau example
We discuss fluxes of long-lived supersymmetric (SUSY) particles produced in the atmosphere from ultra-high energy cosmic-ray interactions with air nuclei. We consider long-lived particle production which proceeds first via the on-shell formation of heavier particles in the SUSY spectrum and then their decays. Specifically, we focus on the production of stau pairs from the decays of squarks produced in the initial cosmic ray-air collision under the purview of gauge-mediated symmetry breaking models that have the stau as the next-to-lightest SUSY particle. The calculation of the resulting stau flux schematically mirrors that of prompt atmospheric neutrino production, however, with the energy scale of initial hadronic collision set to EeV energy scales of the incident cosmic rays rather than the PeV energies where the prompt atmospheric neutrino fluxes dominate over neutrino fluxes from pions and kaons, and with the appropriate stau production cross section. We show the effect of accounting for the energy distribution of the staus relative to the squark energy distributions. We discuss the potential for future ultra-high energy detectors similar in scope to IceCube-Gen2 to detect atmospheric staus via tracks going through the detector volume. Current collider constraints on stau pair production within the SUSY framework considered here are more constraining than those from a detector like IceCube-Gen2 over ten years.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
32 examples of LLM applications in materials science and chemistry: towards automation, assistants, agents, and accelerated scientific discovery
Abstract Large language models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 32 total projects developed during the second annual LLM hackathon for applications in materials science and chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.
Computer Science↗
Influence of inhomogeneous stochasticity on the falsifiability of mean-field theories and examples from accretion disc modelling
ABSTRACT Despite spatial and temporal fluctuations in turbulent astrophysical systems, mean-field theories can be used to describe their secular evolution. However, observations taken over time scales much shorter than dynamical time scales capture a system in a single state of its turbulence ensemble. Comparing with mean-field theory can falsify the latter only if the theory is additionally supplied with a quantified precision. The central limit theorem provides appropriate estimates to the precision only when fluctuations contribute linearly to an observable and with constant coherent scales. Here, we introduce an error propagation formula that relaxes both limitations, allowing for non-linear functional forms of observables and inhomogeneous coherent scales and amplitudes of fluctuations. The method is exemplified in the context of accretion disc theories, where inhomogeneous fluctuations in the surface temperature are propagated to the disc emission spectrum – the latter being a non-linear and non-local function of the former. The derived precision depends non-monotonically on emission frequency. Using the same method, we investigate how binned spectral fluctuations in telescope data change with the spectral resolving power. We discuss the broader implications for falsifiability of a mean-field theory.
79 ASTRONOMY AND ASTROPHYSICS↗
Robustness of electronic screening effects in electron spectroscopies: Example of V 2 O 5
In bulk and low-dimensional extended systems, the screening of excitations by the electron cloud is a key feature governing spectroscopic properties. Widely used computational approaches, especially in the framework of many-body perturbation theory, such as the GW approximation and the resulting approximate Bethe-Salpeter equation, are explicitly formulated in terms of the screened Coulomb interaction. In the present work, we explore the effect of screening in absorption and electron energy loss spectroscopy, concentrating on the effect of local distortions on the screening and elucidating the resulting changes in the various spectra. Using the layered bulk oxide V 2 O 5 as prototype material, we show in which way local distortions affect the screening, and in which way changes in the screening impact electron energy loss and absorption spectra including excitons. We highlight cancellations that make many-body effects in the spectra very robust with respect to structural modifications, while the band structure undergoes significant changes and the nature of the excitations may also be affected. Here, this yields insight concerning the structure-properties relations that are crucial for the use of V 2 O 5 as energy storage material, and more generally, that may be used to optimize the analysis and the calculation of electronic spectra in complex materials.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗