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Chemical Reaction Networks Explain Gas Evolution Mechanisms in Mg-Ion Batteries
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Hard–Soft Acid–Base Theory Explains Photoexcited Carrier Dynamics in Porphyrin/CNT Nanohybrids: Time-Domain Atomistic Analysis
We employ the fundamental chemical concepts of hard− soft acid−base to formulate general principles governing excited-state dynamics in zinc porphyrin (ZnP)/carbon nanotube (CNT) hybrids for energy photoconversion. Atomistic quantum dynamics simulations demonstrate that electron-withdrawing and donating substituents at the ZnP β-pyrrolic position strongly influence the dynamics. ZnP photoexcitation produces subpicosecond electron transfer (ET) from ZnP to CNT, in agreement with the experiment. Substitutions of CN by H and tBu accelerate the ET. The trend is directly related to the hard−soft acid−base concept because the soft−soft interaction between the t Bu- ZnP acid and the mild CNT base enhances the donor−acceptor coupling. Longer coherence and more active vibrational modes facilitate the ET in t Bu-ZnP/CNT. Electron−hole recombination in CN-ZnP/CNT occurs on a hundred picosecond time scale, nicely corroborated by the experiment. The exciton lifetime is extended beyond a nanosecond by the substitutions. The soft−soft interaction in t Bu-ZnP/ CNT increases the splitting between the highest occupied orbitals of the two subsystems, reduces their mixing, and decreases nonadiabatic coupling between the ground and excited states. Rapid decoherence and involvement of low-frequency vibrations favor longer lifetimes. Our investigation reveals that larger p K a of the β-pyrrolic acid gives rapid ET and slow recombination and provides detailed mechanistic information, essential for future optoelectronic applications.
Identifying Key Environmental Factors Explaining Temporal Patterns of DOC Export From Watersheds in the Conterminous United States
The export of dissolved organic carbon (DOC) from a watershed is a key component of the terrestrial biosphere carbon cycle. There is a need to improve our understanding of how and by how much various environmental factors are driving the temporal patterns of DOC export in order to accurately model and evaluate terrestrial carbon storage and fluxes. In this synthesis, we compiled observational data sets from 14 watersheds in the conterminous United States spanning the time period from 1981 to 2017. We used these data sets to examine the relative impacts of various climate, atmospheric deposition, and land cover factors on the temporal patterns of DOC export across watersheds of different sizes and landscape conditions, as well as the time-series autocorrelation of DOC export. Overall, our results suggest that the dominant factor on an annual scale was the amount of precipitation, which had a positive correlation with DOC export from a watershed. Overall increasing nitrogen deposition was coincident with increasing DOC export, and increasing sulfur deposition was coincident with declining DOC export. The seasonal pattern of DOC export was strongly regulated by air temperature, the long-term trend was negatively influenced by increasing sulfur deposition, and no obvious autocorrelation was detected in DOC export. In addition, higher rates of DOC export were positively correlated with greater area of wetlands within a watershed, but was not found to be strongly related to any of the other land cover types.
Potential Vorticity Dynamics Explain How Extratropical Oceans and the Arctic Modulate Wintertime Land–Temperature Variations
Temperature variations across the continental northern hemisphere at the interdecadal scale are thought to be remotely modulated by oceanic internal climate variability and the Arctic. Nevertheless, further elucidating the dynamics is essential for clarifying ongoing debates. We show that potential vorticity (PV) dynamics provide a concise explanation for these teleconnections. Our findings demonstrate that extratropical oceans and the Arctic can remotely modulate the wintertime continental temperature variations by stimulating PV anomalies, which are constrained by climatological PV gradients and jet streams. A causal explanation includes anomalous temperature and precipitation over oceans and the Arctic inducing local PV anomalies via diabatic heating. Subsequently, meridional and downstream advection distributes the anomalous PV to remote land regions where the climatological PV gradients are strong, that is, involving PV fronts, as well as jet streams; therefore, PV fronts and jet streams jointly indicate land regions that are largely and frequently impacted. However, land can also modulate other regions through the same mechanism when variations over land occur in advance. Clear causality depends on which factor is independent, while interactions among those regions may convolute the causality, thereby causing further debates.
Explaining Forcing Efficacy With Pattern Effect and State Dependence
The magnitude of global surface temperature change in response to unit radiative forcing depends on the type and magnitude of forcing agent—a concept known as a “forcing efficacy.” However, the mechanisms behind the forcing efficacy are still unclear. In this study, we perform a set of simulations using CESM1 to calculate the efficacy of 10 different forcing agents defined in terms of fixed-SST effective radiative forcing, and then use a Green's function approach to show that each forcing efficacy can be largely understood in terms of the radiative feedbacks associated with the different surface temperature patterns induced by the forcing agents (a pattern effect). We also quantify how the state dependence of feedbacks on global mean surface temperature anomalies impacts forcing efficacies. The results show that the forcing efficacy can be well reconstructed with a combination of pattern effect and state dependence.
High Spatial Melt Rate Variability Near the Totten Glacier Grounding Zone Explained by New Bathymetry Inversion
Totten Glacier is a fast-moving East Antarctic outlet with the potential for significant future sea-level contributions. We deployed four autonomous phase-sensitive radars on its ice shelf to monitor ice-ocean interactions near its grounding zone and made active source seismic observations to constrain gravity-derived bathymetry models. We observe an asymmetry in basal melting with mean melt rates along the grounding zone differing by up to 20 m/a. Our new bathymetry model reveals that this melt rate asymmetry coincides with an asymmetry in water column thickness and that the low-melting ice-shelf portion is shielded from the main cavity circulation. A 2-year record yields year-to-year melt rate variability of 7–9 m/a with no seasonal cycle. Our results highlight the key role of bathymetry near grounding lines for accurate modeling of ice-shelf melt, and the importance of sustained multi-year monitoring, especially at ice-shelf cavities where the dominant melt rate drivers vary primarily inter-annually.
Physical Insights From the Multidecadal Prediction of North Atlantic Sea Surface Temperature Variability Using Explainable Neural Networks
Abstract North Atlantic sea surface temperatures (NASST), particularly in the subpolar region, are among the most predictable in the world's oceans. However, the relative importance of atmospheric and oceanic controls on their variability at multidecadal timescales remain uncertain. Neural networks (NNs) are trained to examine the relative importance of oceanic and atmospheric predictors in predicting the NASST state in the Community Earth System Model 1 (CESM1). In the presence of external forcings, oceanic predictors outperform atmospheric predictors, persistence, and random chance baselines out to 25‐year leadtimes. Layer‐wise relevance propagation is used to unveil the sources of predictability, and reveal that NNs consistently rely upon the Gulf Stream‐North Atlantic Current region for accurate predictions. Additionally, CESM1‐trained NNs successfully predict the phasing of multidecadal variability in an observational data set, suggesting consistency in physical processes driving NASST variability between CESM1 and observations.
(Un)Explained EMIC Waves: Understanding Quiet Time EMIC Wave Drivers
Electromagnetic ion cyclotron (EMIC) waves are known to be generated through cyclotron resonance with the local ion particle population and grow when there is a large enough temperature anisotropy. In general, these temperature anisotropies necessary for wave growth are found to be associated with either solar wind pressure pulses or particle injections during geomagnetic storms or substorms. However, some EMIC events do not show any clear association with these known drivers and appear unexplained. In our analysis of high-amplitude (>1 nT) non-storm time EMIC waves, we find that 24 out of the 223 (~11%) EMIC events with peak amplitude greater than 1 nT were not found to be associated with any clear EMIC wave driver. This raises a compelling question: What magnetospheric or solar wind driver provides the free energy to grow these quiet-time EMIC waves? Here, we examine two EMIC events on 13 April 2017 and 13 February 2014, which were excited during extremely quiet solar wind and geomagnetic conditions. Furthermore, an in-depth analysis of field and particle measurements from multiple data sets, including ground and in situ data for these two events, indicates that extremely weak and otherwise insignificant pressure values and/or very weak substorm injections occurring multiple hours before the event play a significant role in quiet time wave generation.
Pivotal Role of Cloud‐Planetary Boundary Layer Coupling to Explain Contrasting Aerosol‐Cloud Relationships
The radiative effect of aerosol on cloud albedo via altering cloud droplet effective radius (r e ) is a major uncertainty in the Earth's climate system. Remote sensing studies have reported either negative or positive relationships between re and aerosol number concentration (N a ) or other aerosol proxies. However, there are much fewer in situ observational evidences and physical explanation remains elusive for the contrasting N a -r e relationships. Here we quantify the N a -r e relationship by using in situ aircraft measurements, together with a re decomposition method. Our analysis reveals that the cloud-planetary boundary layer (PBL) coupling plays a pivotal role on the N a -r e relationship. Quantitative r e decomposition indicates that the contrasting N a -r e relationships in two cloud-PBL coupling regimes result from different balances of four distinct aspects. The widely recognized number effect may be outweighed by the joint effects of the remaining three that have been rarely investigated and largely ignored in N a -r e parameterizations.
Baseflow Identification via Explainable AI With Kolmogorov‐Arnold Networks
Abstract Hydrological models often involve constitutive laws that may not be optimal in every application. We propose to replace such laws with the Kolmogorov‐Arnold networks (KANs), a class of neural networks designed to identify symbolic expressions. We demonstrate KAN's potential on the problem of baseflow identification, a notoriously challenging task plagued by significant uncertainty. KAN‐derived functional dependencies of the baseflow components on the aridity index outperform their original counterparts; they demonstrate that water availability, rather than potential evapotranspiration, drives baseflow by constraining actual evapotranspiration under arid conditions. On a test set, they increase the Nash‐Sutcliffe efficiency (NSE) by 65%, decrease the root mean squared error by 29%, and increase the Kling‐Gupta efficiency by 34%. This superior performance is achieved while reducing the number of fitting parameters from three to two. Next, we use data from 378 catchments across the continental United States to refine the water‐balance equation at the mean‐annual scale. The KAN‐derived equations based on the refined water balance outperform both the current aridity index model, with up to a 105% increase in NSE, and the KAN‐derived equations based on the original water balance. While the performance of our model and tree‐based machine learning methods is similar, KANs offer the advantage of simplicity and transparency and require no specific software or computational tools. This case study focuses on the aridity index formulation, but the approach is flexible and transferable to other hydrological processes. Plain Language Summary Equations used in hydrologic model are often suboptimal, resulting in reduced prediction accuracy and efficiency. We implemented Kolmogorov‐Arnold networks (KAN), a machine learning algorithm for deriving symbolic formulations, to estimate groundwater recharge and showed that it outperforms an existing state‐of‐the‐art semi‐empirical formulation. In hydrology, Nash‐Sutcliffe efficiency (NSE), root mean squared error (RMSE), and Kling‐Gupta efficiency (KGE) are commonly used to evaluate model performance. Higher NSE and KGE values indicate better performance, while lower RMSE values are preferable. Our results show that NSE increased by 71%, RMSE decreased by 32%, and KGE improved by 25%. In addition, KAN identifies an optimal functional form and can be used to derive new analytical formulas using the prior knowledge. The KAN‐inspired equation outperformed the original formulation and reduced the fitting parameters. Furthermore, we refined the water‐balance equation at the mean‐annual scale and showed that, based on the new water‐balance equation, KAN can derive new formulations that are superior to the original aridity index formulations (up to 105% increase in NSE) and KAN‐derived equations based on the original water balance. These findings highlight the significant potential of KAN to advance the scientific understanding of a wide range of hydrologic processes. Key Points Kolmogorov‐Arnold networks (KANs) enhance interpretability of machine‐learned hydrological models KAN‐derived symbolic formulations outperform state‐of‐the‐art semi‐empirical aridity indices KAN‐identified functional form yields an analytical index with fewer fitting parameters and improved performance
Coupling between oxygen redox and cation migration explains unusual electrochemistry in lithium-rich layered oxides
Abstract not provided
Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism
The endoplasmic-reticulum aminopeptidase ERAP1 processes antigenic peptides for loading on MHC-I proteins and recognition by CD8 T cells as they survey the body for infection and malignancy. Crystal structures have revealed ERAP1 in either open or closed conformations, but whether these occur in solution and are involved in catalysis is not clear. Here, we assess ERAP1 conformational states in solution in the presence of substrates, allosteric activators, and inhibitors by small-angle X-ray scattering. We also characterize changes in protein conformation by X-ray crystallography, and we localize alternate C-terminal binding sites by chemical crosslinking. Structural and enzymatic data suggest that the structural reconfigurations of ERAP1 active site are physically linked to domain closure and are promoted by binding of long peptide substrates. These results clarify steps required for ERAP1 catalysis, demonstrate the importance of conformational dynamics within the catalytic cycle, and provide a mechanism for the observed allosteric regulation and Lys/Arg528 polymorphism disease association.
Sequence-specific dynamic DNA bending explains mitochondrial TFAM’s dual role in DNA packaging and transcription initiation
Abstract Mitochondrial transcription factor A (TFAM) employs DNA bending to package mitochondrial DNA (mtDNA) into nucleoids and recruit mitochondrial RNA polymerase (POLRMT) at specific promoter sites, light strand promoter (LSP) and heavy strand promoter (HSP). Herein, we characterize the conformational dynamics of TFAM on promoter and non-promoter sequences using single-molecule fluorescence resonance energy transfer (smFRET) and single-molecule protein-induced fluorescence enhancement (smPIFE) methods. The DNA-TFAM complexes dynamically transition between partially and fully bent DNA conformational states. The bending/unbending transition rates and bending stability are DNA sequence-dependent—LSP forms the most stable fully bent complex and the non-specific sequence the least, which correlates with the lifetimes and affinities of TFAM with these DNA sequences. By quantifying the dynamic nature of the DNA-TFAM complexes, our study provides insights into how TFAM acts as a multifunctional protein through the DNA bending states to achieve sequence specificity and fidelity in mitochondrial transcription while performing mtDNA packaging.
Aldehyde cool-flame chemistry explains a missing source of organic acids
Combustion emission is a significant source of organic acids, impacting atmospheric chemistry and climate. Their formation mechanisms, however, remain poorly understood, leading to underestimation in kinetic models. We investigate the cool-flame oxidation of key combustion intermediates—C 1 –C 4 aldehydes and benzaldehyde. Using in-situ synchrotron vacuum ultraviolet photoionization mass spectrometry, we observe the direct conversion of aldehydes to organic acids, a process enhanced by HO 2 radicals. Quantum chemistry calculations reveal that the reaction of RC(O)O 2 with HO 2 on the singlet potential energy surface contributes to organic acids. Incorporating this pathway into a kinetic model significantly improves organic acid prediction. Despite the high-temperature nature of engine combustion, significant spatial and temporal inhomogeneities (e.g., near-wall regions and crevice volumes) lead to localized cool-flame conditions, facilitating organic acid formation and emission. Elucidating the acid formation under cool-flame conditions provides a critical mechanism for accurately modelling anthropogenic organic acid emissions and developing mitigation strategies.
Can ferric-oxyl excited states explain elongated iron-oxygen bonds in heme peroxidase catalytic intermediates?
The use of X-ray structures to determine and interpret the ferryl iron-oxygen bond order in molecular oxygen-activating heme enzymes has, in the past, been controversial. This has mainly stemmed from the susceptibility of ferryl species to X-ray-induced electronic state changes. In this work we establishe using time-resolved serial femtosecond X-ray crystallography (tr-SFX) on a dye-decolourising peroxidase that the ferryl intermediate species (Compounds I and II) captured following in situ mixing of microcrystals with H 2 O 2 have single, rather than the double bond character expected. X-ray emission validated tr-SFX data with quantum refinement, time-dependent-DFT calculations and QM/MM geometry optimizations together support the concept that the single iron-oxygen bond character is not an indication of ferryl reduction or a protonated form (Fe IV -OH) but is instead attributed to the existence of accessible excited states possessing ferric-oxyl (Fe III –O •– ) character. Such states offer insight into the nature of ferryl heme.
Ion correlations explain kinetic selectivity in diffusion-limited solid-state synthesis reactions
Establishing viable solid-state synthesis pathways for novel inorganic materials remains a major challenge in materials science. Previous pathway design methods using pairwise reaction approaches have navigated the thermodynamic landscape with first-principles data but lack kinetic information, limiting their effectiveness. This gap leads to suboptimal precursor selection and predictions, especially for reactions forming competing phases with similar formation energies, where ion diffusion is a critical influence. Here we demonstrate an inorganic synthesis framework by incorporating machine learning-derived transport properties through ‘liquid-like’ product layers into a thermodynamic cellular reaction model. In the Ba–Ti–O system, known for its competitive polymorphism, we obtain accurate predictions of phase formation with varying BaO:TiO2 ratios as a function of time and temperature. We find that diffusion–thermodynamics interplay governs phase compositions, with cross-ion transport coefficients critical for predicting diffusion-limited selectivity. This work bridges length scales and timescales by integrating solid-state reaction kinetics with first-principles thermodynamics and spatial reactivity.
Emergent actin flows explain distinct modes of gliding motility
During host infection, Toxoplasma gondii and related unicellular parasites move using gliding, which differs fundamentally from other known mechanisms of eukaryotic cell motility. Gliding is thought to be powered by a thin layer of flowing filamentous (F)-actin sandwiched between the plasma membrane and a myosin-covered inner membrane complex. How this surface actin layer drives the various gliding modes observed in experiments—helical, circular, twirling and patch, pendulum or rolling—is unclear. Here we suggest that F-actin flows arise through self-organization and develop a continuum model of emergent F-actin flow within the confines provided by Toxoplasma geometry. In the presence of F-actin turnover, our model predicts the emergence of a steady-state mode in which actin transport is largely directed rearward. Removing F-actin turnover leads to actin patches that recirculate up and down the cell, which we observe experimentally for drug-stabilized actin bundles in live Toxoplasma gondii parasites. These distinct self-organized actin states can account for observed gliding modes, illustrating how different forms of gliding motility can emerge as an intrinsic consequence of the self-organizing properties of F-actin flow in a confined geometry.