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At least 1,801 records · Page 100

The Role of Seasonality and the ENSO Mode in Central and East Pacific ENSO Growth and Evolution

Abstract A cyclostationary linear inverse model (CSLIM) is used to investigate the seasonal growth of tropical Pacific Ocean El Niño–Southern Oscillation (ENSO) events with canonical, central Pacific (CP), or eastern Pacific (EP) sea surface temperature (SST) characteristics. Analysis shows that all types of ENSO events experience maximum growth toward final states occurring in November and December. ENSO events with EP characteristics also experience growth into May and June, but CP events do not. A single dominant “ENSO mode,” growing from an equatorial heat content anomaly into a characteristic ENSO-type SST pattern in about 9 months (consistent with the delayed/recharge oscillator model of ENSO), is essential for the predictable development of all ENSO events. Notably, its seasonality is responsible for the late-calendar-year maximum in ENSO amplification. However, this ENSO mode alone does not capture the observed growth and evolution of diverse ENSO events, which additionally involve the seasonal evolution of other nonorthogonal Floquet modes. EP event growth occurs when the ENSO mode is initially “covered up” in combination with other Floquet modes. The ENSO mode’s slow seasonal evolution allows it to emerge while the other modes rapidly evolve and/or decay, leading to strongly amplifying and more predictable EP events. CP events develop when the initial state has a substantial contribution from Floquet modes with meridional mode–like SST structures. Thus, while nearly all ENSO events involve the seasonally varying ENSO-mode dynamics, the diversity and predictability of ENSO events cannot be understood without identifying contributions from the remaining Floquet modes. Significance Statement The purpose of this study is to identify structures that lead to seasonal growth of diverse types of El Niño–Southern Oscillation (ENSO) events. An important contribution from this study is that it uses an observationally constrained, empirically derived seasonal model. We find that processes affecting the evolution of diverse ENSO events are strongly seasonally dependent. ENSO events with eastern equatorial Pacific sea surface temperature (SST) characteristics are closely related to a single “ENSO mode” that resembles theoretical models of ENSO variability. ENSO events that have central equatorial Pacific SST characteristics include contributions from additional “meridional mode” structures that evolve via different physical processes. These findings are an important step in evaluating the seasonal predictability of ENSO diversity.

Vimont, Daniel J.↗

Correlated Ion Transport Governed by Dynamic Local Structure in High Concentration and Localized High Concentration Electrolytes

Understanding the dynamics of cluster formation and network percolation provides the mechanistic link between microscopic solvation structure and transport in concentrated electrolytes, including localized high-concentration electrolytes (LHCEs). Although recent studies have shown LHCEs to form micelle-like aggregates at specific compositions, a quantitative understanding of how solvation structures and transport properties depend on salt–solvent–diluent ratios remains limited. Here, we integrate molecular dynamics with Onsager transport analyses to chart the evolution of solvation microstructure and associated ionic transport in LiFSI/DMC/TTE, achieving good agreement with experimental conductivities across composition. We show that micelle formation arises from a dynamic instability of the cation–anion network, and that network percolation is the primary determinant of conductivity. Two compositional thresholds emerge: A critical network concentration (CNC) and a critical micelle concentration (CMC) that delineate transitions from extended percolating networks to micelle-like clusters and then to fragments. These structural transitions rationalize the nonintuitive conductivity decrease at intermediate dilution despite monotonically decreasing viscosity and provide composition-level design rules for LHCEs.

Mohanakrishnan, Rohith Srinivaas [University of Ca↗

Unexpected “Spontaneous” Evolution of Catalytic, MOF-Supported Single Cu(II) Cations to Catalytic, MOF-Supported Cu(0) Nanoparticles

A desirable feature of metal–organic frameworks (MOFs) is their well-defined structural periodicity and the presence of well-defined catalyst grafting sites (e.g., reactive –OH and –OH 2 groups) that can support single-site heterogeneous catalysts. However, one should not overlook the potential role of residual organic moieties, specifically formate ions that can occupy the catalyst anchoring sites during MOF synthesis. Here we show how these residual formate species in a Zr-based MOF, NU-1000, critically alter the structure, redox capability, and catalytic activity of postsynthetically incorporated Cu(II) ions. Single-crystal X-ray diffraction measurements established that there are two structurally distinct types of Cu(II) ions in NU-1000: one type with residual formate and one without. In NU-1000 with formate, Cu(II) solely binds to the node via the formate-unoccupied, bridging μ 3 –OH, whereas in the formate-free case, it displaces protons from two node hydroxo ligands and resides close to the terminal –OH 2 . Under an inert atmosphere, node-bound formate facilitates the unanticipated reduction of isolated Cu(II) to nanoparticulate Cu(0)—a behavior which is essentially absent in the formate-free analogue because no other sacrificial reductant is present. When the two MOFs were tested as benzyl alcohol oxidation catalysts, we observed that residual formate boosts the catalytic turnover frequency. Density functional calculations showed that node-bound formate acts as a sacrificial two-electron donor and assists in reducing Cu(II) to Cu(0) by a nonradical pathway. The negative Gibbs free energy of reaction (ΔG) and enthalpy of reaction (ΔH) indicate that the reduction is thermodynamically favorable. Here, the work presented here highlights how the often-neglected residual formate prevalent in nearly all zirconium-based MOFs can significantly modulate the properties of supported catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evolution of Charge-Lattice Dynamics across the Kuramoto Synchronization Phase Diagram of Quantum Tunneling Polarons in Cuprate Superconductors

Because of its sensitivity to the instantaneous structure factor, S(Q,t = 0), Extended X-ray Absorption Fine Structure (EXAFS) is a powerful tool for probing the dynamic structure of condensed matter systems in which the charge and lattice dynamics are coupled. When applied to hole-doped cuprate superconductors, EXAFS has revealed the presence of internal quantum tunneling polarons (IQTPs). An IQTP arises in EXAFS as a two-site distribution for certain Cu–O pairs, which is also duplicated in inelastic scattering but not observed in standard diffraction measurements. The Cu–Sr pair distribution has been found to be highly anharmonic and strongly correlated to both the IQTPs and to superconductivity, as, for example, in YSr 2 Cu 2.75 Mo 0.25 O 7.54 (T c =84 K). In order to describe such nontrivial, anharmonic charge-lattice dynamics, we have proposed a model Hamiltonian for a prototype six-atom cluster, in which two Cu-apical-O IQTPs are charge-transfer bridged through Cu atoms by an O atom in the CuO 2 plane and are anharmonically coupled via a Sr atom. By applying an exact diagonalization procedure to this cluster, we have verified that our model indeed produces an intricate interplay between charge and lattice dynamics. Then, by using the Kuramoto model for the synchronization of coupled quantum oscillators, we have found a first-order phase transition for the IQTPs into a synchronized, phase-locked phase. Most importantly, we have shown that this transition results specifically from the anharmonicity. Finally, we have provided a phase diagram showing the onset of the phase-locking of IQTPs as a function of the charge-lattice and anharmonic couplings in our model. We have found that the charge, initially confined to the apical oxygens, is partially pumped into the CuO 2 plane in the synchronized phase, which suggests a possible connection between the synchronized dynamic structure and high-temperature superconductivity (HTSC) in doped cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Diversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal symbiosis (AMS) is widespread mutualistic association between plants and fungi, which plays an essential role in nutrient exchange, enhancement in plant stress resistance, development of host, and ecosystem sustainability. Previous studies have shown that plant small secreted proteins (SSPs) are involved in beneficial symbiotic interactions. However, the role of SSPs in the evolution of AMS has not been well studied yet. In this study, we performed computational analysis of SSPs in 60 plant species and identified three AMS-specific ortholog groups containing SSPs only from at least 30% of the AMS species in this study and three AMS-preferential ortholog groups containing SSPs from both AMS and non-AMS species, with AMS species containing significantly more SSPs than non-AMS species. We found that independent lineages of monocot and eudicot plants contained genes in the AMS-specific ortholog groups and had significant expansion in the AMS-preferential ortholog groups. Also, two AMS-preferential ortholog groups showed convergent changes, between monocot and eudicot species, in gene expression in response to arbuscular mycorrhizal fungus Rhizophagus irregularis. Furthermore, conserved cis-elements were identified in the promoter regions of the genes showing convergent gene expression. We found that the SSPs, and their closely related homologs, in each of three AMS-preferential ortholog groups, had some local variations in the protein structural alignment. We also identified genes co-expressed with the Populus trichocarpa SSP genes in the AMS-preferential ortholog groups. This first plant kingdom-wide analysis on SSP provides insights on plant-AMS convergent evolution with specific SSP gene expression and local diversification of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗

Automated phase segmentation and quantification of high-resolution TEM image for alloy design

In the alloy design and development process, a wealth of atomically resolved structural high-resolution transmission electron microscopy (HRTEM) images are produced. Identifying the different nano-precipitate phases and tracking their evolution under various compositions and during manufacturing or post-processing requires hundreds of HRTEM images and thousands of precipitates. The nanoscopic phase information labeling and analysis purely relies on humans are prohibitively costly and time-consuming, sometimes not reliable because of the lack of authoritative knowledge. Here, in this work, we develop a novel unsupervised machine learning approach coupled with adaptive computer vision techniques with features in the Fourier space to automatically determine the number of phases and segment/quantify the phases with nanoscale resolution, allowing for quantitative correlation between nanostructure formation, processing and functional properties. To automate the phase extraction/quantification and ascertain its applicability, we have applied the developed framework to the HRTEM images from several alloy systems, processing conditions, image magnifications, and phase types and morphologies (precipitates, nano-twins, stacking faults, crystalline matrix, and amorphous structures) for verification. This study paves the road for compression, visualization, and translation of raw image structural data into physically relevant information in real-time with minimal human supervision. It shows the promise of enabling high-throughput materials characterization for the acceleration of alloy manufacturing and design.

36 MATERIALS SCIENCE↗

The Impact of Catalyst Layer Composition and Structure on Performance and Durability of PEMWE Anodes

A study of various compositions of anodes for proton exchange membrane water electrolysis aimed at reducing precious metal content and system costs without compromising performance and durability is presented. A key challenge in current water electrolysis technologies is the reliance on high iridium loadings to ensure sufficient catalytic activity, electronic conductivity, and durability for the oxygen evolution reaction. To address this, catalyst layers based on the stable but kinetically limited rutile phase of iridium oxide are combined with platinum nanoparticles and carbon-based additives to improve structural properties and ink processability. By systematically varying the volume ratios of carbon to precious metals and ionomer to solids, compositional trends have been identified, and significant performance improvements have been achieved. Structural and elemental analysis confirms improved dispersion of platinum and iridium can be achieved, as well as electronic conductivity improvements within the catalyst layer. Polarization curve analysis has shown the ability of added Pt and C to significantly increase catalytic activity. These results highlight the potential positive impact of Pt and C on anode structure, composition, and cell performance.

36 MATERIALS SCIENCE↗

Exploring the Spatial Control of Topotactic Phase Transitions Using Vertically Oriented Epitaxial Interfaces

Engineering oxygen vacancy formation and distribution is a powerful route for controlling the oxygen sublattice evolution that affects diverse functional behavior. The controlling of the oxygen vacancy formation process is particularly important for inducing topotactic phase transitions that occur by transformation of the oxygen sublattice. Here we demonstrate an epitaxial nanocomposite approach for exploring the spatial control of topotactic phase transition from a pristine perovskite phase to an oxygen vacancy-ordered brownmillerite (BM) phase in a model oxide La 0.7 Sr 0.3 MnO 3 (LSMO). Incorporating a minority phase NiO in LSMO films creates ultrahigh density of vertically aligned epitaxial interfaces that strongly influence the oxygen vacancy formation and distribution in LSMO. Combined structural characterizations reveal strong interactions between NiO and LSMO across the epitaxial interfaces leading to a topotactic phase transition in LSMO accompanied by significant morphology evolution in NiO. Using the NiO nominal ratio as a single control parameter, we obtain intermediate topotactic nanostructures with distinct distribution of the transformed LSMO-BM phase, which enables systematic tuning of magnetic and electrical transport properties. The use of self-assembled heterostructure interfaces by the epitaxial nanocomposite platform enables more versatile design of topotactic phase structures and correlated functionalities that are sensitive to oxygen vacancies.

36 MATERIALS SCIENCE↗

3D Printed Nickel–Molybdenum-Based Electrocatalysts for Hydrogen Evolution at Low Overpotentials in a Flow-Through Configuration

Three-dimensional (3D) printed, hierarchically porous nickel molybdenum (NiMo) electrocatalysts were synthesized and evaluated in a flow-through configuration for the hydrogen evolution reaction (HER) in 1.0 M KOH(aq) in a simple electrochemical H-cell. 3D NiMo electrodes possess hierarchically porous structures because of the resol-based aerogel precursor, which generates superporous carbon aerogel as a catalyst support. Relative to a traditional planar electrode configuration, the flow-through configuration allowed efficient removal of the hydrogen bubbles from the catalyst surface, especially at high operating current densities, and significantly decreased the overpotentials required for HER. An analytical model that accounted for the electrokinetics of HER as well as the mass transport with or without the flow-through configuration was developed to quantitatively evaluate voltage losses associated with kinetic overpotentials and ohmic resistance due to bubble formation in the porous electrodes. Furthermore, the chemical composition, electrochemical surface area (ECSA), and roughness factor (RF) were also systematically studied to assess the electrocatalytic performance of the 3D printed, hierarchically porous NiMo electrodes. An ECSA of 25163 cm2 was obtained with the highly porous structures, and an average overpotential of 45 mV at 10 mA cm–2 was achieved over 24 h by using the flow-through configuration. The flow-through configuration evaluated in the simple H-cell achieved high electrochemical accessible surface areas for electrochemical reactions and provided useful information for adaption of the porous electrodes in flow cells.

08 HYDROGEN↗

Microscopic Theory of Long-Time Center-of-Mass Self-Diffusion and Anomalous Transport in Ring Polymer Liquids

We construct a microscopic theory at the level of segment-scale correlated space–time intermolecular forces for the long-time center-of-mass (CM) diffusion constant and intermediate-time non-Fickian transport in dense solutions and melts of ring polymers. The approach combines ideas of polymer, colloid, and liquid-state statistical mechanics to quantify how the multifractal intra-ring conformational structure and inter-ring packing correlations determine dynamic caging constraints and time-dependent friction. Breakdown of Rouse theory is predicted to occur due to length scale-dependent temporal correlation of forces exerted on pairs of tagged ring segments from surrounding polymers. At large enough degrees of polymerization (N), a stronger scaling of the CM diffusion constant (D ∝ N –2 ) is predicted, with a crossover N D proportional to the product of the system-specific macromolecular volume fraction and dimensionless compressibility. In analogy with caging effects in glass-forming fluids, the theory does appear to begin to fail at sufficiently high N/N D for the center-of-mass diffusivity, likely due to another crossover to an even slower activated transport regime. However, use of N/N D with the theoretically predicted N D , in conjunction with dynamic blob scaling ideas for local Rouse friction, collapses semidilute and concentrated solution simulation data onto a master curve. Based on the same physical ideas employed to predict the diffusion constant, a generalized Langevin equation description is formulated for intermediate-time CM transport. It predicts two subdiffusive regimes that emerge due to the self-similar nature of internal ring structure. Analytic and numerical predictions for the apparent non-Fickian exponent as a function of time, N/N D and dimensionless compressibility, the evolution of the maximum degree of subdiffusive motion with N/N D , and the time scale for recovering Fickian diffusion are made, all of which are in good accordance with melt simulations. Furthermore, the present work sets the stage to address activated dynamics and glass formation on the macromolecular scale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thin‐Film Ferroelectrics

Abstract Over the last 30 years, the study of ferroelectric oxides has been revolutionized by the implementation of epitaxial‐thin‐film‐based studies, which have driven many advances in the understanding of ferroelectric physics and the realization of novel polar structures and functionalities. New questions have motivated the development of advanced synthesis, characterization, and simulations of epitaxial thin films and, in turn, have provided new insights and applications across the micro‐, meso‐, and macroscopic length scales. This review traces the evolution of ferroelectric thin‐film research through the early days developing understanding of the roles of size and strain on ferroelectrics to the present day, where such understanding is used to create complex hierarchical domain structures, novel polar topologies, and controlled chemical and defect profiles. The extension of epitaxial techniques, coupled with advances in high‐throughput simulations, now stands to accelerate the discovery and study of new ferroelectric materials. Coming hand‐in‐hand with these new materials is new understanding and control of ferroelectric functionalities. Today, researchers are actively working to apply these lessons in a number of applications, including novel memory and logic architectures, as well as a host of energy conversion devices.

Fernandez, Abel↗

Conceptual Designs for Irradiation Creep Testing of SiC in HFIR

Understanding irradiation creep of nuclear fuel cladding is important to properly size the initial fuel-cladding gap and understand when pellet-cladding contact is expected to occur due to a combination of fuel swelling and cladding creep-down. Irradiation creep also plays a role in relaxing stresses that develop in-pile. Silicon carbide fiber–reinforced silicon carbide matrix (SiC/SiC) composites are the leading long-term accident-tolerant fuel cladding concept for light-water reactors (LWRs). Although some limited data are available regarding irradiation creep of the individual constituents (fibers, matrix), data regarding irradiation creep of SiC/SiC composites are currently insufficient. Additional data regarding irradiation creep compliance and the rupture lifetime (combination of creep and slow crack growth) are needed to understand material limitations. This work describes the design and development of two irradiation vehicles that are being pursued for testing SiC/SiC concepts in the High Flux Isotope Reactor (HFIR). The first is a passive experiment, referred to as the PRECISE experiment, that leverages the constant coolant pressure of HFIR to compress a metallic bellows and provide a well-characterized load to drive creep in a SiC/SiC dog bone specimen. The total creep strain would be quantified post-irradiation by measuring dimensional changes of the specimen length as well as local dimensional changes within the gauge region. Non-stressed specimens would also be irradiated under the same conditions to provide an indication of dimensional changes due to radiation-induced swelling in the absence of creep. A second, more complex experiment, referred to as the INSITE experiment, is being designed in parallel that would use pneumatics to pressurize a metal bellows and linear variable differential transformers (LVDTs) to measure the specimen displacement in situ during irradiation. Such an experiment would provide significantly more data regarding the evolution of the creep compliance as a function of dose and applied stress within a single experiment but would require significantly more development time and cost to execute. The primary concern with the INSITE experiment is the accuracy, reliability, and expected lifetime of the LVDTs during irradiation at elevated temperatures. Efforts are being made to adjust the experiment design and operating procedure to limit LVDT temperatures and mitigate or otherwise compensate for uncertainties due to factors such as temperature fluctuations, creep in the surrounding structural materials, and drift of the LVDTs. This work describes the experiment designs, thermal and structural analysis that were performed to ensure that the desired temperature and stress conditions can be achieved, some initial sensitivity analyses to predict the evolution of the radiation-induced specimen displacements, and potential sources of uncertainty in the measurements. Out-of-pile testing is being performed in parallel to confirm that the test trains achieve the expected stress states in the specimens and do not result in prohibitive stress concentrators (e.g., in the grip regions) that might risk pre-mature failure. The PRECISE experiments are proceeding toward fabrication and assembly with HFIR insertion planned during fiscal year 2026. The INSITE experiment is progressing toward out-of-pile demonstrations, which will provide more conclusive evidence regarding the feasibility of executing these tests in HFIR or whether alternative displacement monitoring techniques may need to be considered.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Constraints on the IBEX Ribbon’s Origin from Its Evolution over a Solar Cycle

Abstract In 2009, the Interstellar Boundary Explorer (IBEX) discovered a narrow “ribbon” of energetic neutral atom emissions across the sky with properties correlated with the solar wind latitudinal structure and the interstellar magnetic field draped around the heliosphere. It is widely believed that the ribbon is formed from the escape of heliospheric ENAs into the local interstellar medium and their eventual return as secondary ENAs. However, there is no consensus on the rate of pitch angle scattering of these PUIs before they become secondary ENAs. We test two opposing limits of scattering rates (“weak” versus “strong”) by solving a time-dependent model of the ribbon that evolves with the solar cycle, and we compare them to IBEX observations over 2009–2019. First, we find that both models qualitatively reproduce the evolution of IBEX fluxes for most of the data set, with a few exceptions, although the strong (or “spatial retention”) scattering model greatly underestimates the observed fluxes. Regardless, time dependence of fluxes cannot distinguish these models. Second, the ribbon’s geometric properties, i.e., its center and radius, are significantly different between the models. The spatial retention model reproduces the observed ribbon centers as a function of energy and time slightly better than the weak scattering model, and the spatial retention model reproduces the observed ribbon radius over energy and time almost perfectly, whereas the weak scattering model compares poorly. Our analysis favors the spatial retention mechanism as the source of the IBEX ribbon, but it requires modification to increase the flux of ENAs observed at 1 au.

Zirnstein, E. J. (ORCID:0000000172400618)↗

Microstructural evolution in Cu-Nb processed via friction consolidation

Immiscible alloys, whether in well-mixed or layered forms, are of increasing interest based on their novel structural and functional properties, such as enhanced thermal stability against grain growth or radiation-induced defect trapping at the interfaces. To address the need for new approaches to tailor microstructures, the microstructural development of an immiscible Cu-Nb alloy processed via friction consolidation of elemental powders is investigated. Friction consolidation is a solid-phase processing technique that imparts severe plastic strain into a deforming volume resulting in elevated temperatures below the melting temperature of the alloy. Two distinct processing pathways were chosen to understand the effect of thermomechanical conditions on the final microstructure. The microstructure was characterized using scanning electron microscopy, scanning transmission electron microscopy, and X-ray diffraction techniques. Path 1 exhibited larger strain, strain rate, and temperature as compared with path 2. In path 1, agglomerated Nb particles were present in the recrystallized ultrafine-grained Cu matrix, while in path 2 extremely fine and dispersed Nb particles were present in a highly deformed Cu matrix. In both pathways, supersaturation of Cu in Nb lattices was noted, but not vice-versa. The asymmetry in mixing is explained based on deformation-based, thermodynamic and kinetic factors. These findings provide a pathway for creation of novel tailored microstructures and improved properties in any number of binary immiscible alloy systems.

Cu-Nb alloys, Microstructural refinement, Friction↗

CuCr 2 O 4 particle growth and evolution across sol–gel routes and calcination profiles

CuCr 2 O 4 spinel is a candidate coating material for central receivers in concentrating solar power to protect structural alloys against high temperature oxidation and related degradation. Coating performance and microstructure of dip-coated and sintered coatings is dictated by the initial particle size of the CuCr 2 O 4 and sintering temperature, but can be compromised by particle agglomeration. Here in this study, sub-micron particles were synthesised through the Pechini and modified Pechini sol–gel methods. Phase composition was confirmed via X-ray diffraction. Particle growth during calcination of the nanoparticles at different temperatures (650°C, 750°C, 850°C) and times (between 1 and 24 h) was measured via laser diffraction and scanning electron microscopy. The modified Pechini method displayed evidence of smaller particle sizes and greater agglomeration. The kinetics of particle growth observed are consistent with a diffusion limited inhibited grain growth model.

36 MATERIALS SCIENCE↗

Structural stability, dihydrogen bonding, and pressure-induced polymorphic transformations in hydrazine borane

Hydrazine borane (N 2 H 4 BH 3 ) has attracted considerable interest as a promising solid-state hydrogen storage material owing to its high hydrogen content and easy preparation. In this work, pressure-induced phase transitions of N 2 H 4 BH 3 were investigated using a combination of vibrational spectroscopy, X-ray diffraction, and density functional theory (DFT) up to 30 GPa. Our results showed that N 2 H 4 BH 3 exhibits remarkable structural stability in a very broad pressure region up to 15 GPa, and then two phase transitions were identified: the first one is from the ambient-pressure Pbcn phase to a Pbca phase near 15 GPa; the second is from the Pbca phase to a Pccn phase near 25 GPa. As revealed by DFT calculations, the unusual stability of N 2 H 4 BH 3 and the late phase transformations were attributed to the pressure-mediated evolutions of dihydrogen bonding frameworks, the compressibility and the enthalpies of the high-pressure polymorphs. In conclusion, our findings provide new insight into the structures and bonding properties of N 2 H 4 BH 3 that are important for hydrogen storage applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning

Abstract Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of the S-states, the resolved structures are a convolution from different catalytic states. Here, we train Decision Tree Classifier and K-means clustering models on Mn compounds obtained from the Cambridge Crystallographic Database to predict the S-state of the X-ray, XFEL, and CryoEM structures by predicting the Mn’s oxidation states in the oxygen-evolving complex. The model agrees mostly with the XFEL structures in the dark S 1 state. However, significant discrepancies are observed for the excited XFEL states (S 2 , S 3, and S 0 ) and the dark states of the X-ray and CryoEM structures. Furthermore, there is a mismatch between the predicted S-states within the two monomers of the same dimer, mainly in the excited states. We validated our model against other metalloenzymes, the valence bond model and the Mn spin densities calculated using density functional theory for two of the mismatched predictions of PSII. The model suggests designing a more optimized sample delivery and illumiation systems are crucial to precisely resolve the geometry of the advanced S-states to overcome the noncoherent S-state transition. In addition, significant radiation damage is observed in X-ray and CryoEM structures, particularly at the dangler Mn center (Mn4). Our model represents a valuable tool for investigating the electronic structure of the catalytic metal cluster of PSII to understand the water splitting mechanism.

Plant Sciences↗

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