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Correction to “COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins”

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Molecular interactions↗

Strong, Nonresonant Radiation Enhances Cis–Trans Photoisomerization of Stilbene in Solution

Previously, it has been demonstrated that external electric fields may be used to exert control over chemical reactivity. In this paper, the impact of a strong, nonresonant IR field (1064 nm) on the photoisomerization of cis-stilbene is investigated in cyclohexane solution. The design of a suitable reaction vessel for characterization of this effect is presented. The electric field supplied by the pulsed, near-IR radiation (ε 1 = 4.5 × 10 7 V/cm) enhances the cis → trans photoisomerization yield at the red edge of the absorption spectrum (wavelengths between 337 and 340 nm). Within the microliter focal volume, up to 75% of all cis-stilbene molecules undergo isomerization to trans-stilbene in the strong electric-field environment, indicating a significant increase relative to the 35% yield of trans-stilbene under field-free conditions. This result correlates with a 1–3% enhancement in the trans-stilbene concentration throughout the bulk solution. Theoretical analysis suggests that the observed change is the result of dynamic Stark shifting of the ground and first excited states, leading to a significant redshift in cis-stilbene’s absorption spectrum. The predicted increase in the absorption cross section in this range of excitation wavelengths is qualitatively consistent with the experimental increase in trans-stilbene production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data-Centric Development of Lignin Structure–Solubility Relationships in Deep Eutectic Solvents Using Molecular Simulations

Lignin is a natural source of aromatic chemicals with significant potential as an abundant, renewable feedstock for value-added products. Deep eutectic solvents (DES)–solvents composed of a hydrogen bond donor (HBD) and acceptor (HBA) in varying ratios–have emerged as a highly tunable class of solvents for lignin solubilization. However, the variety of possible DES compositions and limited molecular-scale understanding of lignin solubility makes solvent selection a challenge without laborious trial-and-error experimentation. To address these challenges, we use classical molecular dynamics (MD) simulations to study the interactions of lignin model compounds with various DES–water systems. Quantitative parameters (descriptors) were calculated by postprocessing the MD results and used to train a regression model that predicts experimentally determined solubilities of lignin model compounds. This approach revealed that the most important descriptors of solubility are the system temperature, solute hydrophilicity, and metrics quantifying hydrogen bonding. Maximizing the interactions between solute–HBD (hydrophobic group), water–HBD (hydrophilic group), and water–HBA molecules led to the highest model compound solubility. Our results support a hydrotropic mechanism in which extensive DES–water hydrogen bonding and favorable HBD interactions with the solute promote high solubility. We applied the regression model derived using model compounds to predict the solubility of representative lignin oligomers. The model predicted lignin oligomers’ solubilities in good agreement with experiments, indicating that the simulations of model compounds can be extended to predict the solubility of larger lignin compounds across a range of solvent compositions and temperatures. Furthermore, these findings provide new molecular-scale insight into lignin solubilization mechanisms and a new method for computationally screening potential solvent systems for lignin valorization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Superresolved Motions of Single Molecular Catalysts during Polymerization Show Wide Distributions

The motion of single molecular ruthenium catalysts during and after single turnover events of ring-opening metathesis polymerization is imaged through single-molecule superresolution tracking with a positional accuracy of ±32 nm. This tracking is achieved through the real-time incorporation of spectrally tagged monomer units into active polymer chain ends during living polymerization; thus, by design, only active-catalyst motion is detected and imaged, without convolution by inactive catalysts. The catalysts show diverse individualistic diffusive behaviors with respect to time that persist for up to 20 s. Catalysts occupy three mobility populations: quasi-stationary (23%), intermediate (53%, 65 nm), and large (24%, 145 nm) step sizes. Differences in catalyst mobility populations also exist between individual aggregates (p < 0.001). Such differential motion indicates widely different local catalyst microenvironments during the catalytic turnover. These mobility differences are uniquely observable through single-catalyst microscopy and are not measurable through traditional ensemble analytical techniques for characterizing the behavior of molecular catalysts, such as nuclear magnetic resonance spectroscopy. The measured distributions of active molecular catalyst motions would not be readily predictable through modeling or first-principles, and the range likely impacts individual catalyst turnover rate and selectivity. This range plausibly contributes to property distributions observable in bulk polymers, such as molecular weight polydispersity (e.g., 1.9 in this system), leading to a revised understanding of the mechanistic, microscale origins of macroscale polymer properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Role of Non-Local Effects on Surface Sensible Heat Flux Under Different Types of Thermal Structures Over the Arctic Sea-Ice Surface

The effects of atmospheric thermal structure on the surface energy flux are poorly understood over the Arctic sea-ice surface. Here, we explore the mechanism of sensible heat exchange under different types of thermal structures over the Arctic sea-ice surface by using data collected during the Multidisciplinary drifting Observatory for the Study of Arctic Climate expedition. The quadrant analysis indicates that strong surface temperature inversions below 100 m enhance non-local effects on the positive (upward) sensible heat flux ($\overline{w'θ'}$) through entrainment of large eddies from the convective boundary layer aloft. However, strong surface inversions restrict the contributions of large eddies to the negative (downward) $\overline{w'θ'}$ due to intensified surface stability. By inspecting the existing parameterization schemes, we found that the European Center for Medium-Range Weather Forecasts Integrated Forecasting System scheme fails to predict the impacts of non-local processes on the positive $\overline{w'θ'}$, and an adjustment term to correct the bias of parameterized $\overline{w'θ'}$ is proposed.

54 ENVIRONMENTAL SCIENCES↗

Revealing core-valence interactions in solution with femtosecond X-ray pump X-ray probe spectroscopy

Abstract Femtosecond pump-probe spectroscopy using ultrafast optical and infrared pulses has become an essential tool to discover and understand complex electronic and structural dynamics in solvated molecular, biological, and material systems. Here we report the experimental realization of an ultrafast two-color X-ray pump X-ray probe transient absorption experiment performed in solution. A 10 fs X-ray pump pulse creates a localized excitation by removing a 1 s electron from an Fe atom in solvated ferro- and ferricyanide complexes. Following the ensuing Auger–Meitner cascade, the second X-ray pulse probes the Fe 1 s → 3 p transitions in resultant novel core-excited electronic states. Careful comparison of the experimental spectra with theory, extracts +2 eV shifts in transition energies per valence hole, providing insight into correlated interactions of valence 3 d with 3 p and deeper-lying electrons. Such information is essential for accurate modeling and predictive synthesis of transition metal complexes relevant for applications ranging from catalysis to information storage technology. This study demonstrates the experimental realization of the scientific opportunities possible with the continued development of multicolor multi-pulse X-ray spectroscopy to study electronic correlations in complex condensed phase systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Three-dimensional flat bands in pyrochlore metal CaNi 2

Electronic flat-band materials host quantum states characterized by a quenched kinetic energy. These flat bands are often conducive to enhanced electron correlation effects and emergent quantum phases of matter. Long studied in theoretical models, these systems have received renewed interest after their experimental realization in van der Waals heterostructures and quasi-two-dimensional (2D) crystalline materials. An outstanding experimental question is if such flat bands can be realized in three-dimensional (3D) networks, potentially enabling new materials platforms and phenomena. Here we investigate the C15 Laves phase metal CaNi 2 , which contains a nickel pyrochlore lattice predicted at a model network level to host a doubly-degenerate, topological flat band arising from 3D destructive interference of electronic hopping. Using angle-resolved photoemission spectroscopy, we observe a band with vanishing dispersion across the full 3D Brillouin zone that we identify with the pyrochlore flat band as well as two additional flat bands that we show arise from multi-orbital interference of Ni d -electrons. Furthermore, we demonstrate chemical tuning of the flat-band manifold to the Fermi level that coincides with enhanced electronic correlations and the appearance of superconductivity. Extending the notion of intrinsic band flatness from 2D to 3D, this provides a potential pathway to correlated behaviour predicted for higher-dimensional flat-band systems ranging from tunable topological to fractionalized phases.

36 MATERIALS SCIENCE↗

Molecular diversity of dissolved organic matter reflects macroecological patterns in river networks

Deciphering dissolved organic matter (DOM) molecular complexity is crucial for understanding ecosystem function. Using the continental-scale Worldwide Hydrobiogeochemistry Observation Network for Dynamic Rivers Systems (WHONDRS) Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) dataset, we reveal fundamental scaling patterns of DOM chemodiversity with watershed characteristics. Analysis of 54 river sites shows local and regional watershed features significantly influence DOM chemodiversity (2500–8718 unique formulae), exhibiting consistent scaling patterns across compound classes and a novel latitudinal gradient (decreasing diversity with increasing latitude). Scaling relationships for DOM composition vary by compound class. Crucially, the scaling parameters (B, baseline chemodiversity; Z, sensitivity) are linearly interrelated. This B–Z relationship is most robust for potentially bio-labile carbohydrates (coefficient of determination R 2 ≈ 0.85), diminishing for recalcitrant, plant-derived molecules (such as lignin), and indicates (potential) biolability-dependent coupling between baseline diversity and environmental responsiveness. These quantitative scaling relationships, with scaling exponents ranging from − 2.1 to 2.2 across compound classes, enable prediction of DOM composition across watersheds, offering a framework to understand ecosystem responses to environmental change. This research bridges biogeochemistry and ecology, providing tools to anticipate molecular transformations across scales.

59 BASIC BIOLOGICAL SCIENCES↗

Creating ground truth for nanocrystal morphology: a fully automated pipeline for unbiased transmission electron microscopy analysis

Control over colloidal nanocrystal morphology (size, size distribution, and shape) is important for tailoring the functionality of individual nanocrystals and their ensemble behavior. Despite this, traditional methods to quantify nanocrystal morphology are laborious. New developments in automated morphology classification will accelerate these analyses but the assessment of machine learning models is limited by human accuracy for ground truth, causing even unsupervised machine learning models to have inherent bias. Herein, we introduce synthetic image rendering to solve the ground truth problem of nanocrystal morphology classification. By simulating 2D images of nanocrystal shapes via a function of high-dimensional parameter space, we trained a convolutional neural network to link unique morphologies to their simulated parameters, defining nanocrystal morphology quantitatively rather than qualitatively. An automated pipeline then processes, quantitatively defines, and classifies nanocrystal morphology from experimental transmission electron microscopy (TEM) images. Using improved computer vision techniques, 42,650 nanocrystals were identified, assessed, and labeled with quantitative parameters, offering a 600-fold improvement in efficiency over best-practice manual measurements. Further, a classification algorithm was trained with a prediction accuracy of 99.5%, which can successfully analyze a range of concave, convex, and irregular nanocrystal shapes. The resulting pipeline was applied to differentiating two syntheses of nominally cuboidal CsPbBr 3 nanocrystals and uniquely classifying binary nickel sulfide nanocrystal phase based on morphology. This pipeline provides a simple, efficient, and unbiased method to quantify nanocrystal morphology and represents a practical route to construct large datasets with an absolute ground truth for training unbiased morphology-based machine learning algorithms.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

The Convergence of Vehicle Electrification and Automation - Enabling Sustainable Automated Mobility Districts

The transportation industry is entering a new frontier with three major simultaneous transformations: electrification, automation, and on-demand services. All three directly affect the same spaces of vehicle technology, infrastructure, and system operational performance. Further, each area of change adds its own driving forces of complexity to the others' design challenges. This paper explores these transformations, framing the implications for vehicle technology and infrastructure and their impact on operating concepts and strategies, which in turn impact the sustainability of the transportation infrastructure in the built environment. Specifically, this paper examines battery-electric vehicles operating in a fully automated fleet within an "automated mobility district" (AMD) setting with multiple on-demand services. From this examination, the paper assesses the implications for transportation electrification, comparing and contrasting traditional fixed-route services with those of on-demand transit and automated transit networks, including the trade-offs between vehicle range (battery capacity), charging parameters, power availability, and operations predictability with respect to policy and infrastructure configurations. The paper also addresses the configuration and management of boarding and alighting zones (also called pickup and drop-off zones), and the need for complementary infrastructure intelligence at intersections and curbs. Finally, conclusions are drawn with respect to the system integration and analysis needs for AMDs regarding resilience and sustainability of mobility infrastructure.

ADVANCED PROPULSION SYSTEMS↗

Inviscid damping of an elliptical vortex subject to an external strain flow

Inviscid spatial Landau damping is studied experimentally for the case of oscillatory motion of a two-dimensional vortex about its elliptical equilibrium in the presence of an applied strain flow. Here, the experiments are performed using electron plasmas in a Penning–Malmberg trap. They exploit the isomorphism between the two-dimensional Euler equations for an ideal fluid and the drift-Poisson equations for the plasma, where plasma density is the analog of vorticity. Perturbed elliptical vortex states are created using E x B strain flows, which are generated by applying voltages to electrodes surrounding the plasma. Measurements of spatial Landau damping (also called critical-layer damping) are in agreement with previous studies in the absence of an applied strain, where the damping is due to a resonance between the local fluid motion and the vortex oscillations. Interestingly, the damping rate does not change significantly over a wide range of applied strain rates. This can be accurately predicted from the initial vorticity profile, even though the resonant frequency is reduced substantially due to the applied strain. For higher amplitude perturbations, nonlinear trapping oscillations also exhibit behavior similar to the strain-free case. In principle, higher-order effects of the applied strain, such as separatrix crossing of peripheral vorticity and interactions with harmonics of the fundamental resonance, are expected to change the damping rate. However, this occurs only for conditions that are not realized in the experiments described here. Vortex-in-cell simulations are used to investigate the possible roles of these effects.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The growth of density perturbations in the last ~10 billion years from tomographic large-scale structure data

In order to investigate the origin of the ongoing tension between the amplitude of matter fluctuations measured by weak lensing experiments at low redshifts and the value inferred from the cosmic microwave background anisotropies, we reconstruct the evolution of this amplitude from z ~ 2 using existing large-scale structure data. To do so, we decouple the linear growth of density inhomogeneities from the background expansion, and constrain its redshift dependence making use of a combination of 6 different data sets, including cosmic shear, galaxy clustering and CMB lensing. We analyze these data under a consistent harmonic-space angular power spectrum-based pipeline. We show that current data constrain the amplitude of fluctuations mostly in the range 0.2 < z < 0.7, where it is lower than predicted by . This difference is mostly driven by current cosmic shear data, although the growth histories reconstructed from different data combinations are consistent with each other, and we find no evidence of systematic deviations in any particular experiment. In spite of the tension with , the data are well-described by the model, albeit with a lower value of S 8 ≡ σ 8 (Ω m /0.3) 0.5 . As part of our analysis, we find constraints on this parameter of S 8 = 0.7781 ± 0.0094 (68% confidence level), reaching almost percent-level errors comparable with CMB measurements, and 3.4σ away from the value found by .

79 ASTRONOMY AND ASTROPHYSICS↗

Got plenty of nothing: cosmic voids as a probe of particle dark matter

The search for a particle dark matter signal in terms of radiation produced by dark matter annihilation or decay has to cope with the extreme faintness of the predicted signal and the presence of masking astrophysical backgrounds. It has been shown that using the correlated information between the dark matter distribution in the Universe with the fluctuations of the cosmic radiation fields has the potential to allow setting apart a pure dark matter signal from astrophysical emissions, since spatial fluctuations in the radiation field due to astrophysical sources and dark matter emission have different features. The cross-correlation technique has been proposed and adopted for dark matter studies by looking at dark matter halos (overdensities). Here in this paper we extend the technique by focusing on the information on dark matter distribution offered by cosmic voids, and by looking specifically at the gamma-ray dark matter emission: we show that, while being underdense and therefore producing a reduced emission as compared to halos, nevertheless in voids the relative size of the cross-correlation signal due to decaying dark matter vs. astrophysical sources is significantly more favourable, producing signal-to-background ratios S/B (even significantly) larger than 1 for decay lifetimes up to 2 × 10 30 s. This is at variance with the case of halos, where S/B is typically (even much) smaller than 1. We show that forthcoming galaxy surveys such as Euclid combined with future generation gamma-ray detectors with improved specifications have the ability to provide a hint of such a signal with a predicted significance up to 5.7σ for galaxies and 1.6σ for the cosmic shear. The bound on the dark matter lifetime attainable exploiting voids is predicted to improve on current bounds in a mass range for the WIMP of 25 ÷ 900 GeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Real singlet scalar benchmarks in the multi-TeV resonance regime

Scalar extensions of the Standard Model (SM) are of much interest at the Large Hadron Collider (LHC) and future colliders. In particular, these models can give rise to resonant di-Higgs production and alter the Higgs trilinear coupling. In this paper, we study di-Higgs production in the Standard Model extended by a real scalar singlet with no additional symmetries. We determine how large the resonant di-Higgs rate and variation in the Higgs trilinear coupling can be in four scenarios: current LHC results and projected results at the high luminosity LHC (HL-LHC), the HL-LHC combined with a circular 𝑒 − ⁢𝑒 + collider such as the Circular Electron Positron Collider or Future Circular Collider with electron-positron collisions, and the HL-LHC combined with a linear 𝑒 − ⁢𝑒 + collider such as the International Linear Collider. While these are updated results from a previous study by [I. M. Lewis and M. Sullivan, Benchmarks for double Higgs production in the singlet extended standard model at the LHC, Phys. Rev. D 96, 035037 (2017).] using current LHC data, we go further and find benchmark points in the multi-TeV resonance regime for future colliders beyond the HL-LHC. Considering current LHC results, the resonant di-Higgs rate can still be an order of magnitude larger than the SM predicted di-Higgs rate. In the HL-LHC scenario, the Higgs trilinear coupling can still be a factor of three larger than the SM prediction for resonance masses in the 1.5–3.5 TeV range, where resonant searches may have less reach. This enhancement is just at the projected 2⁢𝜎 sensitivity of the HL-LHC. We find there are resonance masses for which the change in the Higgs trilinear is maximized while the resonant rate is negligible. We provide an analytical understanding of these effects with a discussion on the interplay of various constraints on the parameter space and the Higgs trilinear coupling.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Detailed study of quark-hadron duality in spin structure functions of the proton and neutron

Background: The response of hadrons, the bound states of the strong force (QCD), to external probes can be described in two different, complementary frameworks: as direct interactions with their fundamental constituents, quarks and gluons, or alternatively as elastic or inelastic coherent scattering that leaves the hadrons in their ground state or in one of their excited (resonance) states. The former picture emerges most clearly in hard processes with high momentum transfer, where the hadron response can be described by the perturbative expansion of QCD, while at lower energy and momentum transfers, the resonant excitations of the hadrons dominate the cross section. The overlap region between these two pictures, where both yield similar predictions, is referred to as quark-hadron duality and has been extensively studied in reactions involving unpolarized hadrons. Some limited information on this phenomenon also exists for polarized protons, deuterons, and 3 He nuclei, but not yet for neutrons. Purpose: In this paper, we present comprehensive and detailed results on the correspondence between the extrapolated deep inelastic structure function g 1 of both the proton and the neutron with the same quantity measured in the nucleon resonance region. Thanks to the fine binning and high precision of our data, and using a well-controlled perturbative QCD (pQCD) fit for the partonic prediction, we can make quantitative statements about the kinematic range of applicability of both local duality and global duality. Method: We use the most updated QCD global analysis results at high x from the Jefferson Lab Angular Momentum Collaboration to extrapolate the spin structure function g 1 into the nucleon resonance region and then integrate over various intervals in the scaling variable x. We compare the results with the large data set collected in the quark-hadron transition region by the CLAS Collaboration, including, for the first time, deconvoluted neutron data, integrated over the same intervals. We present this comparison as a function of the momentum transfer Q 2 . Results: We find that, depending on the integration interval and the minimum momentum transfer chosen, a clear transition to quark-hadron duality can be observed in both nucleon species. Furthermore, we show, for the first time, the approach to scaling behavior for g 1 measured in the resonance region at sufficiently high momentum transfer. Conclusions: Here, our results can be used to quantify the deviations from the applicability of pQCD for data taken at moderate energies and can help with extraction of quark distribution functions from such data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Strain-Induced Quantum Phase Transitions in Magic-Angle Graphene

In this work, we investigate the effect of uniaxial heterostrain on the interacting phase diagram of magic-angle twisted bilayer graphene. Using both self-consistent Hartree-Fock and density-matrix renormalization group calculations, we find that small strain values (ε~0.1%-0.2%) drive a zero-temperature phase transition between the symmetry-broken "Kramers intervalley-coherent" insulator and a nematic semimetal. The critical strain lies within the range of experimentally observed strain values, and we therefore predict that strain is at least partly responsible for the sample-dependent experimental observations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Measurement of In-Medium Jet Modification Using Direct Photon + Jet and 𝜋 0 + Jet Correlations in 𝑝 + 𝑝 and Central Au + Au Collisions at $\sqrt{s_{NN}}$ = 200 GeV

The STAR Collaboration presents measurements of the semi-inclusive distribution of charged-particle jets recoiling from energetic direct-photon (𝛾 dir ) and neutral-pion (𝜋 0 ) triggers in 𝑝 + 𝑝 and central Au + Au collisions at $\sqrt{s_{NN}}$ =2 00 GeV over a broad kinematic range, for jet resolution parameters 𝑅 = 0.2 and 0.5. Medium-induced jet yield suppression is observed to be larger for 𝑅 = 0.2 than for 0.5, reflecting the angular range of jet energy redistribution due to quenching. The predictions of model calculations incorporating jet quenching are not fully consistent with the observations. Furthermore, these results provide new insight into the physical origins of jet quenching.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Antiphase boundary migration as a diffusion mechanism in a P3 sodium layered oxide

The electrode materials of Na-ion batteries must exhibit fast ion transport, a property that is often negatively impacted when mobile cations order. Many layered Na (and K) intercalation compounds adopt the P3 crystal structure, which tends to stabilize cation-vacancy orderings over a wide range of Na concentrations. The ordered phases have been predicted to consist of domains that are periodically separated by antiphase boundaries (APBs) to accommodate variations in Na concentration. The mechanisms and rates with which Na diffuses within such ordered phases of P3 are not understood. We have conducted a first-principles study of Na diffusion in the P3 structure, using Na x CoO 2 as a model system. We find that most simple nearest-neighbor hops in Na-vacancy ordered phases in P3 result in unstable configurations and are therefore forbidden. We identify an alternative mechanism of Na transport that is mediated by APB migration via the formation and expansion of kinks along domain boundaries. The limiting kinetic barriers for this mechanism are quite low (0.03 to 0.30 eV). Vacancy defects are not required, and furthermore have formation energies that are higher than those of the APB kink defects. Furthermore, our results suggest that APB migration is a fundamental diffusion mechanism in the P3 structure.

36 MATERIALS SCIENCE↗