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DOE OSTI2025

Unfolding of the Villin Headpiece Domain: Revealing Structural Heterogeneity with Time‐Resolved X‐Ray Solution Scattering and Markov State Modeling

Understanding protein folding pathways is crucial to deciphering the principles of protein structure and function. Here, the unfolding dynamics of the 35‐residue villin headpiece (HP35) and a norleucine‐substituted variant (2F4K) using a combination of experimental and computational techniques is investigated. Time‐resolved X‐ray solution scattering coupled with equilibrium molecular dynamics simulations and Markov state modeling reveals distinct unfolding mechanisms between the two variants: HP35 and 2F4K. Specifically, HP35 exhibits a two‐state unfolding process, whereas an intermediate state is identified for the 2F4K mutant. A Markov state model constructed from simulations is used to map atomic‐level transitions to experimental observations, providing insights into the role of sequence variations in modulating folding pathways. The findings underscore the importance of integrating experimental and computational approaches to unravel protein unfolding mechanisms between heterogenous structural ensembles.

Nijhawan, Adam K. [Department of Chemistry Northwe↗
DOE OSTI2022

How galaxies populate halos in extreme density environments: An analysis of the halo occupation distribution in SDSS

Recent works have shown that the properties of galaxy populations in simulated dark matter halos vary with large-scale environments. These results suggest a variation in the halo occupation distribution (HOD) in extreme density environments since the dynamical and astrophysical conditions prevailing in these regions may significantly affect the formation and evolution of their halos and residing galaxies, influencing the mean number of satellite galaxies. To analyse these effects, we identify cosmic voids and future virialised structures (FVS) in the Sloan Digital Sky Server Data Release 12 (SDSS-DR12) and estimate the HOD within these super-structures using group catalogues as dark matter halo proxies. Our goal is to use observational galaxy data to characterise the HOD within cosmic voids and FVS, explore the different properties of these galaxies populations and compare them with the general results outside these super-structures. We use a publicly available observational galaxy catalogue with information on redshifts, positions, magnitudes and other astrophysical features to build a volume complete galaxy sample and identify cosmic voids and FVS. Using a publicly available galaxy group catalogue as a proxy to dark matter halos, we compute the HOD within both types of super-structures for different absolute magnitude thresholds. We also study the dependence on the results on the main void and FVS properties, density and volume. We also analysed the main characteristics of the stellar content of galaxies inside these extreme-density regions such as the mean stellar age and the galaxy light concentration index. In all cases, we compare the results with those derived from the Field sample, defined by objects outside both types of environments. Inside cosmic voids, we find a strong decrease in HOD concerning the Field results. In the most extreme cases, the mean number of satellites fall to ~ 50%. Inside FVS, the HOD shows a significant increase to the Field, with a ~ 40% excess in the mean number of satellites. These results are present for the different galaxy luminosity ranges explored. In both environments, the differences with respect to the Field increases for the extreme values of the density environments. However, we obtain no signs of variations related to intrinsic characteristics of the super-structures, indicating that the effects depend mainly on the density of the large-scale environment. In addition, we find that the cumulative distribution of the mean age of stars of the central galaxy also varies in the different regions, this suggests that the history of the formation of the dark matter halos may be different. Finally, we explore the HOD for the 25% youngest (oldest) galaxies, based on the mean age of their stars. We find that for the low-mass groups the youngest galaxies are only present inside voids and are generally central galaxies. On the other hand, for the high-mass groups the FVS environments show the same increase in the HOD concerning the Field as previously mentioned. We find that cosmic voids lack a significant fraction of galaxies with the oldest stellar population.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

On Properties of Adjoint Systems for Evolutionary PDEs

We investigate the geometric structure of adjoint systems associated with evolutionary partial differential equations at the fully continuous, semi-discrete, and fully discrete levels and the relations between these levels. We show that the adjoint system associated with an evolutionary partial differential equation has an infinite-dimensional Hamiltonian structure, which is useful for connecting the fully continuous, semi-discrete, and fully discrete levels. We subsequently address the question of discretize-then-optimize versus optimize-then-discrete for both semi-discretization and time integration, by characterizing the commutativity of discretize-then-optimize methods versus optimize-then-discretize methods uniquely in terms of an adjoint-variational quadratic conservation law. For Galerkin semi-discretizations and one-step time integration methods in particular, we explicitly construct these commuting methods by using structure-preserving discretization techniques.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Stronger field-emission science via coupling novel nanoscale imaging techniques

We implemented a vacuum field emission electron microscope (FEM) using the electron optics of a low-energy /photoemission electron microscope (LEEM/PEEM). Historically, there have been other FEM hardware platforms, and the distinctive feature of our method is that it integrates with the LEEM/PEEM and associated techniques, enabling a powerful multi-capability toolset for studying fundamental materials properties underpinning field emission (FE) and vacuum arc initiation. Typically, LEEM is used to image surface structure, which influences both work function and electric field distribution near a surface, while PEEM is used to map photoelectric work function across a surface. Our FEM adds the capability for spatially-correlated coincident-site measurements of FE currents to go-along with structure and work function. LEEM, PEEM, and our FEM implementation achieve nanoscale spatial resolution relevant for materials studies in nanoscience/engineering. Our approach requires a straightforward calibration of the electron optics to enable focused FEM imaging under intentional electric field variation. We demonstrate the FEM approach by imaging field emitter arrays relevant for vacuum nanoelectronics. We demonstrate submicron spatial resolution and dynamic measurement of FE versus applied electric field. We anticipate this capability will enable fundamental structure-function studies of FE and arc initiation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Constructing uniform oxygen defect engineering on primary particle level for high-stability lithium-rich cathode materials

Lithium-rich layered cathode materials are considered to be research focus of cathode candidates for next generation lithium-ion batteries due to their high specific capacity and low cost. However, lattice deoxidation associated with elemental migration and internal local shrinkage usually results in deteriorated cyclic performance and notorious voltage attenuation, severely limiting its application. In this paper, we have successfully injected uniform oxygen defects into surface region of Li 1.2 Ni 0.13 Co 0.13 Mn 0.54 O 2 primary particles under the high-pressure and weak carbonate environment. Various experimental investigations indicate that the injected robust oxygen defects can not only mitigate detrimental interfacial reactions but also suppress unfavorable lattice variation and particle breakage. More importantly, theoretical calculations unravel the critical roles of oxygen defects in regulating energy band structure for strengthened anionic reversibility. Owing to stabilization effects of unique oxygen defect engineering, the modified Li 1.2 Ni 0.13 Co 0.13 Mn 0.54 O 2 cathode has harvested dramatically enhanced electrochemical performance including a high initial coulombic efficiency of 96.6%, an outstanding capacity retention of 91.96% (1C, 200 cycles) and suppressed voltage decay of only 1.62 mV per cycle. Therefore, this facile and effective defect engineering strategy could establish new guidance for promoting practical application of Li-rich Mn-based cathode material.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

A highly-stable layered Fe/Mn-based cathode with ultralow strain for advanced sodium-ion batteries

Sodium-ion batteries (SIBs) with iron- and manganese-based cathode electrodes have exhibited great promise in the grid-scale energy storage systems, on the basis of the satisfactory theoretical capacity, as well as huge abundance, low price and non-toxicity of raw materials. However, the inferior cycle life of cathode materials originating from their poor structural stability remains a formidable challenge towards practical applications. In this study, an efficient strategy of improving the structure durability is demonstrated in iron- and manganese-based cathodes by dual heteroatom doping. The as-obtained P2-type Na 0.65 Li 0.08 Cu 0.08 Fe 0.24 Mn 0.6 O 2 cathode delivers superior cyclability (88.2% capacity retention for 500 cycles at 2C), fabulous rate capability (76% capacity retention at 5C compared to 0.1C), and a useable reversible capacity of around 85 mAh g -1 at 0.1C. Through in-depth characterizations, the underlying structure-property relationship is established, revealing that the complete solid-solution reaction during cycling ensures the ultralow volume variation (as small as 0.7%) and excellent electrochemical performance. These results highlight the significance of fabricating a stable host for the design and development of advanced SIBs with long life.

25 ENERGY STORAGE↗
DOE OSTI2025

Morphological Heterogeneity Impact of Film Solid-State Cathode on Utilization and Fracture Dynamics

Structural heterogeneity in solid-state batteries can impact material utilization and fracture mechanisms. Crystallographically oriented lithium cobalt oxide film cathodes serve as a model electrode system for exploring how void distribution contributes to stress relief and build up during cycling. Real- and reciprocal-space operando and ex situ synchrotron based experiments are utilized to understand structural changes across multiple length scales contribute to stress generation and fracture. Nanotomography uncovers a depth-dependent porosity variation in the pristine electrode and highlights preferential fracture in regions of lower porosity during delithiation. Energy-dispersive X-ray diffraction and 3D X-ray absorption near-edge spectroscopy (XANES) reveal the underutilization of cathode material in these regions. 3D XANES also confirms preferential delithiation near the sub-grain boundaries. Chemo-mechanical modeling coupled with site-specific mechanical characterization demonstrate how stress accumulation in dense regions of the electrode leads to fracture and underutilization of active material. In conclusion, our findings reveal the importance of materials design to alleviate stress in small-volume changing cathodes.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Using metacommunity ecology to understand environmental metabolomes

Abstract Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics ‘meta-metabolome ecology’ and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Intrinsic and extrinsic conduction contributions at nominally neutral domain walls in hexagonal manganites

Conductive and electrostatic atomic force microscopy (cAFM and EFM) are used to investigate the electric conduction at nominally neutral domain walls in hexagonal manganites. The EFM measurements reveal a propensity of mobile charge carriers to accumulate at the nominally neutral domain walls in ErMnO3, which is corroborated by cAFM scans showing locally enhanced direct current conductance. Our findings are explained based on the established segregation enthalpy profiles for oxygen vacancies and interstitials, providing a microscopic model for previous, seemingly disconnected observations ranging from insulating to conducting behavior. In addition, we observe variations in conductance between different nominally neutral walls that we attribute to deviations from the ideal charge-neutral structure within the bulk, leading to a superposition of extrinsic and intrinsic contributions. Our study clarifies the complex transport properties at nominally neutral domain walls in hexagonal manganites and establishes the possibility to tune their electronic response based on oxidation conditions, opening the door for domain-wall-based sensor technology.

Schultheiß, J. (ORCID:0000000173891295)↗
DOE OSTI2022

Dynamical electron correlation and the chemical bond. I. Covalent bonds in AH and AF (A = B–F)

Dynamical electron correlation has a major impact on the computed values of molecular properties and the energetics of molecular processes. This study focused on the effect of dynamical electron correlation on the spectroscopic constants ($R$ e , $ω$ e , $D$ e ), and potential energy curves, Δ$E$($R$), of the covalently bound AH and AF molecules, A = B–F. The changes in the spectroscopic constants (Δ$R$ e , Δ$ω$ e , Δ$D$ e ) caused by dynamical correlation are erratic and, at times, even surprising. These changes can be understood based on the dependence of the dynamical electron correlation energies of the AH and AF molecules as a function of the bond distance, i.e., Δ$E$ DEC ($R$). At large $R$, the magnitude of Δ$E$ DEC ($R$) increases nearly exponentially with decreasing $R$, but this increase slows as $R$ continues to decrease and, in many cases, even reverses at very short $R$. The changes in Δ$E$ DEC ($R$) in the region around $R$ e were as unexpected as they were surprising, e.g., distinct minima and maxima were found in the curves of Δ$E$ DEC ($R$) for the most polar molecules. The variations in Δ$E$ DEC ($R$) for $R$ ≲ $R$ e are directly correlated with major changes in the electronic structure of the molecules as revealed by a detailed analysis of the spin-coupled generalized valence bond wave function. In conclusion, the results reported here indicate that we have much to learn about the nature of dynamical electron correlation and its effect on chemical bonds and molecular properties and processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Increased electron, positron, and x-ray production from high intensity laser interactions using micro-wire targets

We report increases in energetic electrons, positrons, and x-rays emitted from high-intensity laser interactions (10 18−20 W/cm 2 ) with structured silicon micro-wires on the surface of a 1 mm gold converter target using a 10 ps laser pulse. A total of four different wire configurations are tested, where the gaps (7–28 μm) between the wires and the thicknesses (3–6 μm) of the wires are varied, while the height remains constant (⁠ ~25 μm). We observe the largest enhancement in electrons, positrons, and x-rays with the sparsest wire configurations. The electron temperature (T e ≈6 MeV) remains consistent across all shots, regardless of whether wires or planar targets are used. This suggests that the observed enhancement is due to increased laser light absorption by the accelerated electrons over a long scale length. Two-dimensional particle-in-cell simulations confirm that absorption is significantly enhanced with the wire target. Additionally, specific simulations examining laser pointing on different parts of the wire structure reveal that, while the final electron spectrum remains largely insensitive, the angular distribution is highly sensitive to these variations.

Bremsstrahlung↗
DOE OSTI2025

DESI 2024 II: sample definitions, characteristics, and two-point clustering statistics

We present the samples of galaxies and quasars used for DESI 2024 cosmological analyses, drawn from the DESI Data Release 1 (DR1). We describe the construction of largescale structure (LSS) catalogs from these samples, which include matched sets of synthetic reference ‘randoms’ and weights that account for variations in the observed density of the samples due to experimental design and varying instrument performance. We detail how we correct for variations in observational completeness, the input ‘target’ densities due to imaging systematics, and the ability to confidently measure redshifts from DESI spectra. We then summarize how remaining uncertainties in the corrections can be translated to systematic uncertainties for particular analyses. We describe the weights added to maximize the signalto-noise of DESI DR1 2-point clustering measurements. We detail measurement pipelines applied to the LSS catalogs that obtain 2-point clustering measurements in configuration and Fourier space. The resulting 2-point measurements depend on window functions and normalization constraints particular to each sample, and we present the corrections required to match models to the data. We compare the configuration- and Fourier-space 2-point clustering of the data samples to that recovered from simulations of DESI DR1 and find they are, generally, in statistical agreement to within 2% in the inferred real-space over-density field. The LSS catalogs, 2-point measurements, and their covariance matrices will be released publicly with DESI DR1.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Density streams in the disc winds of Classical T Tauri stars

ABSTRACT Spectral and photometric variability of the Classical T Tauri stars RY Tau and SU Aur from 2013 to 2022 is analysed. We find that in SU Aur the H α line’s flux at radial velocity RV = −50 ± 7 km s−1 varies with a period P = 255 ± 5 d. A similar effect previously discovered in RY Tau is confirmed with these new data: P = 21.6 d at RV = −95 ± 5 km s. In both stars, the radial velocity of these variations, the period, and the mass of the star turn out to be related by Kepler’s law, suggesting structural features on the disc plane orbiting at radii of 0.2 au in RY Tau and 0.9 au in SU Aur, respectively. Both stars have a large inclination of the accretion disc to the line of sight – so that the line of sight passes through the region of the disc wind. We propose there is an azimuthal asymmetry in the disc wind, presumably in the form of ‘density streams,’ caused by substructures of the accretion disc surface. These streams cannot dissipate until they go beyond the Alfven surface in the disc’s magnetic field. These findings open up the possibility to learn about the structure of the inner accretion disc of CTTS on scales less than 1 au and to reveal the orbital distances related to the planet’s formation.

Petrov, P. P. (ORCID:0000000155514963)↗
DOE OSTI2021

Seasonal trends in photosynthesis and leaf traits in scarlet oak

Understanding seasonal variation in photosynthesis is important for understanding and modelling plant productivity. Here, we used shotgun sampling to examine physiological, structural and spectral leaf traits of upper canopy, sun-exposed leaves in Quercus coccinea Münchh (scarlet oak) across the growing season in order to understand seasonal trends, explore the mechanisms underpinning physiological change, and investigate the impact of extrapolating measurements from a single date to the whole season. We tested the hypothesis that photosynthetic rates and capacities would peak at the summer solstice i.e., at the time of peak photoperiod. Contrary to expectations, our results reveal a late-season peak in both photosynthetic capacity and rate before the expected sharp decrease at the start of senescence. This late-season maximum occurred after the higher summer temperatures and VPD, and was correlated with the recovery of leaf water content and increased stomatal conductance. We modelled photosynthesis at the top of the canopy and found that the simulated results closely tracked the maximum carboxylation capacity of Rubisco. For both photosynthetic capacity and modelled top-of-canopy photosynthesis, the maximum value was therefore not observed at the summer solstice. Rather, in each case the measurements at and around the solstice were close to the overall seasonal mean, with values later in the season leading to deviations from the mean by up to 41% and 52% respectively. Overall, we found that the expected Gaussian pattern of photosynthesis was not observed. We conclude that an understanding of species- and environment-specific changes in photosynthesis across the season is essential for correct estimation of seasonal photosynthetic capacity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Structure of open-flavor four-quark states in the charm and bottom region

We present quantitative results for masses and the internal structure of four-quark states with two heavy quarks, i.e., Q Q ′ q ¯ q ¯ ′ with Q , Q ′ ∈ { c , b } and q , q ′ ∈ { u , d , s } , and J P ∈ 1 + . The composition of these states in terms of meson-meson and diquark-antidiquark pairs, extracted from a relativistic four-body Faddeev-Yakubowski equation, is dynamically determined from underlying QCD forces. We find states at energy levels in very good agreement with lattice QCD and, where available, with experimental states. Their internal structure, most notably between the T c c + , T b c and T b b − , show significant and sizeable variations. Published by the American Physical Society 2025

Hoffer, Joshua (ORCID:0009000871793956)↗
DOE OSTI2024

Multiplexed CRISPR-Cas9 mutagenesis of rice PSBS1 noncoding sequences for transgene-free overexpression

Understanding CRISPR-Cas9’s capacity to produce native overexpression (OX) alleles would accelerate agronomic gains achievable by gene editing. To generate OX alleles with increased RNA and protein abundance, we leveraged multiplexed CRISPR-Cas9 mutagenesis of noncoding sequences upstream of the rice PSBS1 gene. We isolated 120 gene-edited alleles with varying non-photochemical quenching (NPQ) capacity in vivo—from knockout to overexpression—using a high-throughput screening pipeline. Overexpression increased OsPsbS1 protein abundance two- to threefold, matching fold changes obtained by transgenesis. Increased PsbS protein abundance enhanced NPQ capacity and water-use efficiency. Across our resolved genetic variation, we identify the role of 5'UTR indels and inversions in driving knockout/knockdown and overexpression phenotypes, respectively. Complex structural variants, such as the 252-kb duplication/inversion generated here, evidence the potential of CRISPR-Cas9 to facilitate significant genomic changes with negligible off-target transcriptomic perturbations. Our results may inform future gene-editing strategies for hypermorphic alleles and have advanced the pursuit of gene-edited, non-transgenic rice plants with accelerated relaxation of photoprotection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Luminescent Zr Complexes with Long-lived Intraligand Charge Transfer Excited States

Understanding and establishing design principles to tune the excited states of earth-abundant sensitizers is crucial for identifying new photosensitizers for sustainable technological advancements. Here, we report a series of three bis Zr (IV) complexes of tridentate, dianionic ligands incorporating two phenoxide donors and aza arene acceptors of increasing electron affinity (pyridine < pyrimidine < pyrazine ) that are air and water-stable. These complexes emit via thermally assisted delayed fluorescence from an intraligand charge transfer excited state with varying metal contributions. The electronic structural changes from different acceptors vary the excited state character and the photophysical properties significantly between the complexes. The variation in photophysics that includes emission lifetime (76 μs to 265 ns), intersystem crossing (ISC) lifetime ( 390 – 290 ps), and the energy difference between the singlet and triplet excited states (∆EST. 170 -100 meV). We observe solvent-independent ISC rates when the excited state has metal contributions (acceptor = pyridine), and the ISC rates vary significantly with solvent polarity when the excited state is an intra-ligand charge transfer state (acceptor = pyrimidine and pyrazine). Transient absorption measurements provided the basis spectra and verified the metal contribution in the excited state. This work provides a basis for developing new sensitizers based on Zr (IV) by providing design principles that can be used to modulate the character of the excited state and its photophysics.

Nattikallungal, Thabassum A. [University of Southe↗
DOE OSTI2024

Light-Induced Charge Separation in Photosystem I from Different Biological Species Characterized by Multifrequency Electron Paramagnetic Resonance Spectroscopy

Photosystem I (PSI) serves as a model system for studying fundamental processes such as electron transfer (ET) and energy conversion, which are not only central to photosynthesis but also have broader implications for bioenergy production and biomimetic device design. In this study, we employed electron paramagnetic resonance (EPR) spectroscopy to investigate key light-induced charge separation steps in PSI isolated from several green algal and cyanobacterial species. Following photoexcitation, rapid sequential ET occurs through either of two quasi-symmetric branches of donor/acceptor cofactors embedded within the protein core, termed the A and B branches. Using high-frequency (130 GHz) time-resolved EPR (TR-EPR) and deuteration techniques to enhance spectral resolution, we observed that at low temperatures prokaryotic PSI exhibits reversible ET in the A branch and irreversible ET in the B branch, while PSI from eukaryotic counterparts displays either reversible ET in both branches or exclusively in the B branch. Furthermore, we observed a notable correlation between low-temperature charge separation to the terminal [4Fe-4S] clusters of PSI, termed F A and F B , as reflected in the measured F A /F B ratio. These findings enhance our understanding of the mechanistic diversity of PSI’s ET across different species and underscore the importance of experimental design in resolving these differences. Though further research is necessary to elucidate the underlying mechanisms and the evolutionary significance of these variations in PSI charge separation, this study sets the stage for future investigations into the complex interplay between protein structure, ET pathways, and the environmental adaptations of photosynthetic organisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗