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At least 19 records

Phosphoserine Charge State Drives Ion Condensation and Spatial Polyamine Presentation in Multirepeat Silaffin

Diatom silaffins direct silica biomineralization through heavily post-translationally modified repeat domains, yet how these modifications reshape the multirepeat conformational ensemble remains unknown. We report all-atom MD simulations of a 195-residue construct spanning repeats R1–R7 of Sil1p from Cylindrotheca fusiformis, carrying the full complement of native PTMs: phosphoserine (pSer), long-chain polyamines (LCPA), dimethyllysine (MLY), and trimethylhydroxylysine phosphate (TPL). We simulated three variants (Native, P1/singly deprotonated phosphate, and P2/doubly deprotonated phosphate) at two NaCl concentrations in triplicate for 500 ns each. All systems disorder from the AlphaFold 3 starting structure. Phosphate charge state, not ionic strength, is the dominant control of ensemble compaction and ion organization. Doubly deprotonated phosphate organizes an extensive Na + condensation shell (∼100 ions, 20% of box Na + ) and a heterogeneous bridging network that integrates both pSer and TPL phosphate groups. The resulting ensemble is compact with LCPA side chains exhibiting above-median solvent accessibility in 84% of simulation frames in P2 at 300 mM. This is higher than any other condition we simulated and indicates that polyamine groups are preferentially surface-presented in the most compact, ion-organized state. A charge-neutralization control confirms that this compact state is a structured intermediate maintained by the bridging network, not a simple collapsed globule. Here, this repeat-scale spatial organization is not captured by single-repeat peptide studies. Understanding the dynamics, mechanism, and spatial organization of PTM-rich silaffin at the repeat scale is a step closer to hierarchical biomimetic materials beyond simple silica morphologies.

Amines↗

Chemo-Mechanical Instabilities in Lithium Cobalt Oxide at Higher State-Of-Charge in Li-Ion Batteries

Transition metal oxide cathodes are widely used in commercial Li-ion batteries. However, their practical charge capacity is limited due to severe chemo-mechanical instabilities at higher charge voltage, and state-of-charge condition. Here, in situ stress and strain measurements were synchronized to probe mechanical deformations in the lithium cobalt oxide (LCO) cathode via a multi-beam stress sensor and digital image correlation, respectively. In situ mechanical measurements revealed how Li removal from the electrode structure induces deformations on the LCO composite cathodes during cycling. The structure and morphology of the LCO cathodes were further investigated by X-ray diffraction (XRD) and scanning electron microscopy (SEM) studies. Two distinct electrochemical and mechanical behaviors were identified when the LCO was charged up to 4.65 V. The LCO undergoes a compressive stress generation when charged up to 4.2 V and surface fractures on the LCO particles were detected by SEM. LCO cathode experienced significantly large contractions (negative strains) when charged up to 4.65 V, where intergranular crack formation and phase transformation were detected on the LCO particles via SEM and XRD, respectively. Overall, the study bridges complicated structural deformations with in situ analysis of mechanical degradations in LCO cathodes charged at higher voltages. The correlation is vital to understanding instability mechanisms in transition metal oxides at high voltages for alkali metal ion batteries.

higher state-of-charge↗

Charge state-dependent ion condensation near conjugated polymer backbones

Despite the technological appeal of polymeric organic mixed ionic/electronic conductors (OMIECs) for diverse applications, a deep understanding of the fundamentals of mixed charge transport in these materials, especially regarding the complex interplay between polymer, ion and solvent structure in determining transport, is lacking. Herein, extensive molecular dynamics (MD) simulations of a model OMIEC representing various electrochemically gated states are reported that reveal charge state-dependent counterion condensation. X-ray diffraction simulations based on the MD data predict a measurable change in the scattering intensity at the counterion absorption edge, indicative of counterion repositioning with charging. We leverage an operando resonant X-ray scattering technique to experimentally corroborate the simulated scattering and report excellent agreement between predicted and experimental data, confirming that counterions preferentially reside in the lamellar mid-plane of crystallites at low doping, and near the polymer backbone at higher doping. Driving forces for ion type-dependent spatial repositioning and implications thereof are discussed.

36 MATERIALS SCIENCE↗

Multilayer film coating for laser ion source target for increase of low charge state production

The use of Laser Ion Source for accelerator facilities has the advantage to tune the characteristic of the produced beams by changing the laser parameters using the same primary target. The advantageous and innovative opportunity to manipulate the characteristic of charge state distributions by the use of composed target, may open new possibilities for the ion sources. In this experiment we characterize and study the plasma produced by the laser ablation of coated targets at constant laser parameters. The performed investigation has the double purpose to have a better understanding of penetration depth of laser in composed materials and understand how to tune the charge states by adding coating films. Finally, the obtained results showed that for particular thickness of coating, the low charge states were produced with higher yield than in the case of pure material.

43 PARTICLE ACCELERATORS↗

Kinetic Control over Disproportionation Stabilizes Wurster’s Blue Catholyte for Nonaqueous Redox Flow Batteries

Redoxmers are organic molecules that serve as charge carriers in redox flow batteries. While these materials are affordable and easy to source, insufficient stability of their charged states (radical ions) remains a challenge. A common reaction of these species is their disproportionation. Furthermore, this reversible reaction yields unstable multiply charged states, shifting the overall charge transfer equilibrium toward the decomposition products. Here we show how kinetic controls can be engineered into a redoxmer molecule to suppress these unwanted charge transfer reactions. This approach is used to transform Wurster's blue, which is historically the first example of a stable radical ion in organic chemistry, into an exceptionally durable redoxmer molecule that persists over thousands of electrochemical cycles.

Cations↗

Analysis of RF Sheath-Driven Tungsten Erosion at RF Antenna in the WEST Tokamak

This study applies the newly developed STRIPE (Simulated Transport of RF Impurity Production and Emission) framework to analyze tungsten (W) erosion at RF antenna structures in the WEST tokamak. STRIPE integrates SolEdge3x for edge plasma backgrounds, COMSOL for 3D RF sheath potentials, RustBCA for sputtering yields, and GITR for impurity transport and ion energy–angle distributions. Building on prior work by Kumar et al. (2025) Nuclear Fusion, 65, 076039, which validated STRIPE for WEST ICRH discharge #57877, the present study provides a spatially resolved assessment of gross W erosion at both Q2 antenna limiters under ohmic and ICRH conditions. Simulations using 2D SolEdge3x profiles in COMSOL capture rectified sheath potentials exceeding 300 V, leading to strong upper-limiter localization. Both poloidal and toroidal asymmetries are observed and attributed to RF sheath effects, with modeled erosion patterns deviating from experiment—highlighting sensitivity to sheath geometry and plasma resolution. Erosion is driven primarily by high-charge-state oxygen ions (O6+–O8+), while D+ plays a negligible role. Assuming a plasma composition of 1% oxygen and 98% deuterium, STRIPE predicts a 30-fold increase in gross W erosion from ohmic to ICRH phases, consistent with a >25-fold rise in W-I (400.9 nm) brightness. Quantitative agreement is within 5% in the ohmic phase and 30% under ICRH, demonstrating predictive capability. Importantly, the study shows that the magnitude of ICRH-driven W erosion depends strongly on the concentration of light impurities (O, B, N, C), which drive sputtering through high charge states. Cleaner plasma conditions with reduced impurity content are therefore expected to substantially mitigate antenna W sources in WEST and other toroidal fusion devices. These findings establish STRIPE as a predictive framework for RF-induced plasma–material interactions and support its application to reactor-scale antenna design.

Kumar, Atul [ORNL] (ORCID:0000000277475210)↗

Integrated modeling of RF-induced tungsten erosion at ICRH antenna structures in the WEST tokamak *

This paper introduces STRIPE (Simulated Transport of RF Impurity Production and Emission), an advanced modeling framework developed to analyze material erosion and the global transport of eroded impurities originating from radio-frequency (RF) antenna structures in magnetic confinement fusion devices. STRIPE integrates multiple physics modules: SolEdge3x for scrape-off-layer plasma profiles, COMSOL for 3D RF rectified sheath potentials, RustBCA for erosion yields and surface interactions, and global impurity transport for 3D ion energy-angle distributions and impurity transport. The framework is applied to an ion cyclotron RF-heated L-mode discharge (#57877) in the WEST tokamak, where it predicts a thirty-fold increase in gross tungsten erosion at antenna limiters during the transition from ohmic to ICRH operation. Additionally, under ICRH conditions, a tenfold enhancement in erosion is observed when comparing RF sheath effects to purely thermal sheath conditions. High-charge-state oxygen ions ($\mathrm{O}$ 6+ and above) are identified as the dominant contributors to tungsten sputtering. To validate the model, a synthetic diagnostic tool based on inverse photon efficiency (S/XB coefficients) from the ColRadPy collisional-radiative model enables direct comparison with spectroscopic measurements. Model predictions using a plasma composition of 1% oxygen and 99% deuterium show good agreement with observed W − I (400.9 nm) emission for discharge #57877, supporting the accuracy of the STRIPE framework. This study focuses specifically on gross erosion calculations to demonstrate STRIPE’s capabilities. Future extensions of this work will incorporate net erosion, re-deposition, self-sputtering effects, and whole-device modeling of sputtered tungsten impurity transport. STRIPE is also being applied to other RF-heated linear and toroidal devices, offering valuable insights for antenna design, impurity control, and performance optimization in next-generation fusion reactors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Estimating Residual Gas Beam Loss in the BNL AGS Booster:Model, Numerical Tools, and Implications for a Polarimeter Chamber

Beamloss from residual gas scattering is calculated for a storage ring of circumference C = 200m, covering a linear magnetic rigidity ramp from B ρ inj = 1.25Tm to B ρ ext = 9.50Tm over tramp = 1.00s. Three loss mechanisms are considered: nuclear inelastic reactions, single Coulomb scattering beyond the acceptance angle of the machine, and charge-state exchange for heavy ions. Calculations are performed for protons and Au 32+ ions, the latter being the charge state delivered by the EBIS pre-injector into the BNL AGS Booster. At a baseline vacuum of P 0 = 5 × 10 −11 mbar the integrated fractional beam loss over the full ramp is negligible for protons (< 0.001%) and 33.1% for Au 32+ . The impact of a 1m polarimeter section at elevated pressure P s = 5 × 10 −9 mbar is evaluated: the proton loss remains negligible, while the Au 32+ loss rises to 45.1%, establishing the vacuum requirement for the polarimeter chamber. In the present compact approximate model, Au 32+ losses are dominated by charge exchange at injection, while proton losses are dominated by single Coulomb scattering. The design, outgassing budget, pumping strategy, and commissioning sequence for a UHV polarimeter chamber housing silicon detectors and ASICs are described in detail.

43 PARTICLE ACCELERATORS↗

Understanding the heat generation mechanisms and the interplay between joule heat and entropy effects as a function of state of charge in lithium-ion batteries

The thermal performance of lithium-ion battery cells is critical for ensuring their safe and reliable operation across various applications. In this study, we employed an isothermal calorimetry method to investigate the heat generation of commercial 18650 lithium-ion battery fresh cells during charge and discharge at different current rates, ranging from 0.05C to 0.5C, and across various temperatures: 20 °C, 30 °C, 40 °C, and 50 °C. Our findings revealed a direct correlation between heat generation and current rates, indicating that higher current rates lead to increased heat generation within the cells. Conversely, we observed that heat generation remained relatively stable as the temperature rose, suggesting that temperature changes within this range may not significantly impact the heat generation of fresh cells during typical operations. Furthermore, our study explored irreversible heat generation, which depends on the applied current and overpotential, using the galvanostatic intermittent titration technique at 0.05C–0.5C and 30 °C. Additionally, electrochemical impedance spectroscopy was performed on the same cells during charge and discharge at 20 °C, 30 °C, and 40 °C to analyze cell impedance. Finally, our results indicated a consistent dependence of impedance on the state of charge and depth of discharge, with a significant increase in impedance observed at the end of the discharge process.

25 ENERGY STORAGE↗

Ca X ML: Chemistry‐informed machine learning explains mutual changes between protein conformations and calcium ions in calcium‐binding proteins using structural and topological features

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of Ca X ML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Demonstration of closed shell breeding of cesium ions with an electron beam ion source

An electron beam ion source serves as a charge breeder for the Californium Rare Isotope Breeder Upgrade (CARIBU) at the Argonne Tandem Linac Accelerator System (ATLAS). The source accepts radioactive beams of 1+ or 2+ ions and raises their charge state for post-acceleration by ATLAS. The efficiency of this process impacts the length of each experiment and, hence, the type and number of experiments that can be run in each program cycle. Recent efforts to improve the charge breeding efficiency for the 80 < A < 160 species typical of CARIBU have focused on utilizing the closed shell breeding technique. Here, with this technique, the electron beam energy is manipulated to take advantage of the large gap in ionization energies at shell closures and selectively populate a single charge state. Charge breeding studies with stable cesium ions have demonstrated an absolute efficiency of 72% for Cs 27+ and a total efficiency of 93%. The Cs 27+ efficiency result represents a factor of 3 improvement over the previous best charge breeding result of 23% for Cs 27+ .

Vondrasek, R. [Argonne National Laboratory (ANL), ↗

Curious cross-field transport effects in multi-ion, magnetized plasma

In contrast to single-ion plasma, multiple-ion-species plasma exhibits new, curious, and large transport effects. On short timescales, where ions exchange momentum, magnetized multi-ion plasma behaves as a most unusual substance, compressible across field lines in number density but incompressible in charge density. It takes 40 times longer for electrons to participate. In this ion–ion cross-field transport regime, we identified the charge-incompressibility heat pump effect, transferring heat both spatially and between species. Curiously, the direction of impurity transport strongly depends on plasma magnetization, characterized by the ratio of light ion gyrofrequency to the collision frequency between light and heavy ion species. The expulsion of heavy ion impurities from a hotspot occurs sufficiently quickly to be observable on MagLIF, so long as plasma becomes sufficiently collisionally magnetized under implosion. Even more curious, multi-ion transport changes its nature in partially ionized plasma, where ions occupy different charge states. In this regime, we identify a partial-ionization deconfinement effect. The combination of cross-field transport, ionization, and recombination leads to a net ion charge moving across magnetic field lines on the ion–ion transport timescale as opposed to the electron–ion transport timescale. Cross-field transport effects in multi-ion plasma are important in a number of applications, including nuclear fusion and plasma mass filters.

Mlodik, M. E. (ORCID:0000000343003941)↗

Systematic improvement of redox potential calculation of Fe(III)/Fe(II) complexes using a three-layer micro-solvation model

Electrochemical transformations of metal ions in aqueous media are challenging to model accurately due to the dynamic solvation structure surrounding ions at different charge states. Predictive modeling at the atomistic scale is essential for understanding these solvation architectures but is often computationally prohibitive. In this contribution, we present a simple, fast, and accurate three-layer micro-solvation model to evaluate the redox potential of metal ions in aqueous solutions. Our model, developed and validated for Fe 3+ /Fe 2+ redox potentials, combines the DFT-based geometry optimizations of the octahedral Fe complex with two layers of explicit water molecules to capture solute–solvent interactions and an implicit solvation model to account for bulk solvent effects. This approach yields accurate predictions for Fe 3+ /Fe 2+ redox potentials in water, achieving errors of 0.02 V with ωB97X-V, 0.01 V with ωB97X-D3, 0.04 V with ωB97M-V, and 0.02 V with B3LYP-D3 functionals. We further demonstrate the generality of our model by applying it to additional metal complexes, including the challenging Fe(CN) 6 3−/4− system, where our model successfully achieves close agreement with experimental values, with an error of 0.07 V and an average error of 0.21 V for all five systems. In summary, the presented simple solvation model has broad applicability and potential for enhancing computational efficiency in redox potential predictions across various chemical and industrial processes of metal ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring Electrode-Level State-of-Charge and State-of-Health Dynamics in Lithium-Ion Battery Cells: Modeling and Experimental Identification

A computationally efficient model serves as a critical prerequisite for battery performance analysis and advanced battery management algorithm design. Although battery models that capture cell-level behavior have been widely explored in existing literature, electrode-level battery models have received much lesser attention till to date. However, such electrode-level models can significantly increase battery performance and life by enabling electrode-level health-conscious control. Such electrode-level control can effectively expand usable energy and power limits of the battery cells by utilizing the knowledge of individual electrodes' charge and health. In this context, this paper presents a comprehensive battery model developed with a reference electrode insertion that captures (i) electrode-level charge/discharge dynamics, (ii) stoichiometric and temporal dependencies of electrode-level resistances, (iii) solid electrolyte interface (SEI) layer growth as key degradation phenomenon, and (iv) capacity fade and resistance rise in each electrode due to nominal battery aging. The proposed model is identified, and a preliminary validation is performed utilizing terminal voltage and negative electrode potential data collected from a pouch cell under one continuous cycling and accelerated aging conditions where the cell experienced 14% capacity loss.

aging↗

Quantum Molecular Charge-Transfer Model for Multistep Auger–Meitner Decay Cascade Dynamics

The fragmentation of molecular cations following inner-shell decay processes in molecules containing heavy elements underpins the X-ray damage effects observed in X-ray scattering measurements of biological and chemical materials, as well as in medical applications involving Auger electron-emitting radionuclides. Traditionally, these processes are modeled using simulations that describe the electronic structure at an atomic level, thereby omitting molecular bonding effects. This work addresses the gap by introducing a novel approach that couples Auger–Meitner decay to nuclear dynamics across multiple decay steps, by developing a decay spawning dynamics algorithm and applying it to potential energy surfaces characterized with ab initio molecular dynamics simulations. We showcase the approach on a model decay cascade following K-shell ionization of IBr and subsequent Kβ fluorescence decay. We examine two competing channels that undergo two decay steps, resulting in ion pairs with a total 3+ charge state. This approach provides a continuous description of the electron transfer dynamics occurring during the multistep decay cascade and molecular fragmentation, revealing the combined inner-shell decay and charge transfer time scale to be approximately 75 fs. In conclusion, our computed kinetic energies of ion fragments show good agreement with experimental data.

Ab initio molecular dynamics↗

Nozzle geometry optimization for high-current aluminum ion beam acceleration via direct plasma injection scheme

We report the generation of a record aluminum ion beam current exceeding 58 mA at the Al 11+ charge state, accelerated to an energy of 5.5 MeV using the direct plasma injection scheme, which integrates a laser ion source (LIS) with a radio frequency quadrupole (RFQ) accelerator. The effect of nozzle geometry on beam extraction was systematically investigated using 8 and 12 mm tapered designs and an 18 mm cylindrical configuration. The 18 mm nozzle achieved the highest Al 11+ beam current, while the 12 mm aperture provided a favorable balance between beam intensity and current density. Beam extraction simulations confirmed effective RFQ matching across multiple charge states, and solenoidal field tuning further enhanced plasma collimation. This work not only establishes a new benchmark for high-current ion beam generation but also provides a fundamental understanding of plasma–beam interface dynamics crucial for the next generation of high-intensity particle accelerators, particularly those employing LIS-RFQ systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Directly Fused Porphyrin‐Tetracyanopentacenequinone Conjugates: Role of the Cross‐Conjugated, Powerful Electron Acceptor in Promoting Highly Efficient Charge Separation

Tetracyanopentacenequinone, a powerful electron acceptor, is fused directly to the porphyrin π-system to create a new class of donor-acceptor conjugates. Owing to the direct fusion and electron-deficient property of tetracyanopentacenequinone, strong intramolecular charge transfer both in the ground and excited states was witnessed. As a control, porphyrin fused with pentacenequinone was also investigated. Upon complete spectral and electrochemical characterization, the excited state properties were initially probed by time-dependent DFT studies, and the occurrence of electron transfer from different excited states was established. Free-energy calculations revealed higher exothermic electron transfer (>600 mV) than the control pentacenequinone-porphyrin systems. Pump-probe studies covering broad spatial and temporal regions revealed efficient excited state charge separation. This was unlike the control pentacenequinone-porphyrin system, where slow charge separation was witnessed only in the case of the zinc derivatives but not the free-base ones, followed by the populating of the triplet excited state. The lifetimes of the charge-separated states ranged between 30–500 ps depending on the solvent and metal ion in the porphyrin cavity. Nanosecond transient absorption studies established the charge recombination path to populate the triplet state of porphyrin or directly to the ground state as a function of solvent polarity and the nature of the conjugate. Furthermore, the significance of cross-conjugated tetracyanopentacenequinone fused directly to the porphyrin π system in promoting highly exothermic and efficient charge separation, irrespective of its cross conjugation, is borne out from this study.

Cross conjugation↗