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DOE OSTI2024

Adaptable SEC‐SAXS data collection for higher quality structure analysis in solution

Abstract The two major challenges in synchrotron size‐exclusion chromatography coupled in‐line with small‐angle x‐ray scattering (SEC‐SAXS) experiments are the overlapping peaks in the elution profile and the fouling of radiation‐damaged materials on the walls of the sample cell. In recent years, many post‐experimental analyses techniques have been developed and applied to extract scattering profiles from these problematic SEC‐SAXS data. Here, we present three modes of data collection at the BioSAXS Beamline 4–2 of the Stanford Synchrotron Radiation Lightsource (SSRL BL4‐2). The first mode, the High‐Resolution mode, enables SEC‐SAXS data collection with excellent sample separation and virtually no additional peak broadening from the UHPLC UV detector to the x‐ray position by taking advantage of the low system dispersion of the UHPLC. The small bed volume of the analytical SEC column minimizes sample dilution in the column and facilitates data collection at higher sample concentrations with excellent sample economy equal to or even less than that of the conventional equilibrium SAXS method. Radiation damage problems during SEC‐SAXS data collection are evaded by additional cleaning of the sample cell after buffer data collection and avoidance of unnecessary exposures through the use of the x‐ray shutter control options, allowing sample data collection with a clean sample cell. Therefore, accurate background subtraction can be performed at a level equivalent to the conventional equilibrium SAXS method without requiring baseline correction, thereby leading to more reliable downstream structural analysis and quicker access to new science. The two other data collection modes, the High‐Throughput mode and the Co‐Flow mode, add agility to the planning and execution of experiments to efficiently achieve the user's scientific objectives at the SSRL BL4‐2.

Matsui, Tsutomu↗

DOE OSTI2025

Streptococcus pneumoniae HtrA is a dynamic and monomeric virulence factor capable of forming larger oligomeric complexes

Abstract High‐temperature requirement A (HtrA) proteases are a conserved family of serine proteases central to protein quality control and bacterial virulence. While Gram‐negative and human HtrAs are structurally well studied, Gram‐positive homologs remain essentially uncharacterized. Here, we present the first integrated structural and mechanistic analysis of a Gram‐positive HtrA, from Streptococcus pneumoniae , a virulence factor essential for adhesion and infection in vivo. Proteomic profiling of an htrA knockout and cleavage assays demonstrate that S. pneumoniae HtrA is required for protein quality control, with the PDZ domain mediating substrate recognition. Biochemically, S. pneumoniae HtrA exists exclusively as a monomer in solution, a striking divergence from canonical trimeric HtrAs that we show is shared with other Gram‐positive homologs. NMR analyses reveal that the monomer dynamically samples open and closed conformations, while cryo‐EM of a catalytic mutant identifies a hexamer stabilized by a unique LoopA–PDZ interaction. Together, these findings define S. pneumoniae HtrA as a dynamic monomer with interdomain coupling between its protease and PDZ domains, establishing Gram‐positive HtrAs as a mechanistically divergent subgroup within the HtrA family.

Lee, Eunjeong [Department of Biochemistry and Mole↗

DOE OSTI2021

Development of an optimized and scalable method for isolation of umbilical cord blood-derived small extracellular vesicles for future clinical use

Abstract Extracellular vesicles (EV) are a promising therapeutic tool in regenerative medicine. These particles were shown to accelerate wound healing, through delivery of regenerative mediators, such as microRNAs. Herein we describe an optimized and upscalable process for the isolation of EV smaller than 200 nm (sEV), secreted by umbilical cord blood mononuclear cells (UCB-MNC) under ischemic conditions and propose quality control thresholds for the isolated vesicles, based on the thorough characterization of their protein, lipid and RNA content. Ultrafiltration and size exclusion chromatography (UF/SEC) optimized methodology proved superior to traditional ultracentrifugation (UC), regarding production time, standardization, scalability, and vesicle yield. Using UF/SEC, we were able to recover approximately 400 times more sEV per mL of media than with UC, and upscaling this process further increases EV yield by about 3-fold. UF/SEC-isolated sEV display many of the sEV/exosomes classical markers and are enriched in molecules with anti-inflammatory and regenerative capacity, such as hemopexin and miR-150. Accordingly, treatment with sEV promotes angiogenesis and extracellular matrix remodeling, in vitro. In vivo, UCB-MNC-sEV significantly accelerate skin regeneration in a mouse model of delayed wound healing. The proposed isolation protocol constitutes a significant improvement compared to UC, the gold-standard in the field. Isolated sEV maintain their regenerative properties, whereas downstream contaminants are minimized. The use of UF/SEC allows for the standardization and upscalability required for mass production of sEV to be used in a clinical setting.

Cardoso, Renato M. S.↗

DOE OSTI2023

Sequential Separation of Linear, Mono–, and Di–Branched Hexane Isomers on a Robust Coordination Polymer with Nonbonding Flexibility

Efficient separation of hexane isomers is a crucial process for upgrading gasoline. Herein, the sequential separation of linear, mono-, and di-branched hexane isomers by a robust stacked 1D coordination polymer termed as Mn-dhbq ([Mn(dhbq)(H 2 O) 2 ], H 2 dhbq = 2,5-dihydroxy-1,4-benzoquinone) is reported. The interchain space of the activated polymer is of optimal aperture size (5.58 Å) that could exclude 2,3-dimethylbutane, while the chain structure can discriminate n-hexane with high capacity (1.53 mmol g –1 at 393 K, 6.67 kPa) by high-density open metal sites (5.18 mmol g –1 ). With the temperature- and adsorbate-dependent swelling of interchain spaces, the affinity between 3-methylpentane and Mn-dhbq can be deliberately controlled from sorption to exclusion, and thus a complete separation of ternary mixture can be achieved. Column breakthrough experiments confirm the excellent separation performance of Mn-dhbq. Furthermore, the ultrahigh stability and easy scalability further highlight the application prospect of Mn-dhbq for separation of hexane isomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Reduction‐induced metal/oxide interfacial sites for selective CO 2 hydrogenation

Abstract The interfacial structures of bimetallic‐derived catalysts play an important role in promoting the activation of reactants such as CO 2 . In particular, both the physical property (e.g., local bonding environment) and the electronic property (e.g., oxidation state) can evolve from their native states under different environments, such as upon reduction and during the catalytic reaction. Hence, taking the CO 2 hydrogenation reaction over Rh‐based catalysts as a case study, the present work compares the interfacial structures in tuning the selectivity toward CH 4 or CO. The combination of ex situ and in situ characterization reveals two representative interfacial structures: the Rh/CeO x interface formed over Rh/CeO 2 is active and selective to produce CH 4 (~95%) by following a formate‐mediated pathway; in comparison, the InO x /Rh interface derived after reduction is active for CO 2 activation and enables a redox mechanism for the exclusive formation of CO (~100%). This work provides insights into the environment‐induced structural evolution at the metal−oxide interfaces, as well as the role of distinct interfacial active sites in tuning the selectivity of CO 2 hydrogenation.

10 SYNTHETIC FUELS↗

DOE OSTI2024

Influence of Rare Earth Ce Additions on Microstructure and Mechanical Properties of Experimental Pipeline Steels

Herein, the effect of Ce additions ranging from 57 to 263 ppm is evaluated for an experimental pipeline steel. Compared to the Ce-free steel, progressive Ce additions result in a slightly refined microstructure, significantly improve transverse impact properties, and slightly increase strength. All these observations can be attributed to the gradual transformation of Mn sulfide and Mn–Si–Al oxide inclusions to Ce-containing oxide/sulfides. In particular, the inclusions consist exclusively of sub-5 μm spherical Ce 2 O 2 S particles upon near-stoichiometric additions of Ce, considering the oxygen and sulfur impurity level of the steel. In conclusion, the results suggest that Ce is a potentially promising alloying addition for next-generation pipeline steels by replacing overtly deleterious inclusions with potentially beneficial ones.

36 MATERIALS SCIENCE↗

DOE OSTI2024

A Machine Learning Approach to Quantitative Analysis of Enamel Microstructure from Scanning Electron Microscopy Images

Dental enamel, the outermost tissue of mammalian teeth, must withstand a lifetime of wear and cyclic contact. To meet this demand, enamel possesses a combination of high hardness and resistance to fracture, properties that are typically mutually exclusive. The impressive damage tolerance has been attributed largely to decussation of the enamel rods, the principal unit of its microstructure. As such, enamel is inspiring the design of next‐generation structural materials. However, quantitative descriptions of the decussated enamel rod microstructure remain limited due to challenges encountered in applying computed tomography and in acquiring quality images appropriate for traditional digital processing methods. Here, a machine learning segmentation method is applied to images of the enamel obtained using scanning electron microscopy to support quantitative analysis of the microstructure. A pretrained convolutional neural network is used to expand the input training image dataset to allow the training of a random forest classifier, which ultimately segments the image with a very small training set ( n = 3 images). A validation of this segmentation method is presented, in addition to its application to calculate relevant microstructural parameters for images of tooth enamel from selected mammalian species. The methodology applied here is equally applicable to other hard tissues.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Tuning Interface Electronic Properties via Chiral Two‐Dimensional Metal‐Organic Frameworks

Control over structural symmetries in nanomaterials offers a powerful approach to engineer electronic properties. For instance, breaking of mirror symmetries in two-dimensional (2D) materials with a hexagonal lattice can lead to nontrivial electronic topologies and correlated-electron phenomena. Yet, the impact of structural chirality on the electronic properties of 2D materials and interfaces remains underexplored. Here, how chiral phases of a 2D metal-organic framework (MOF) with a hexagonal lattice—consisting of hexaazatriphenylene molecules coordinated to Cu atoms—scatter, confine, and perturb the Shockley surface state (SS) electrons of an underlying Ag(111) substrate is investigated. Via low-temperature scanning tunneling microscopy and spectroscopy, noncontact atomic force microscopy, and numerical calculations based on an electronic plane-wave expansion method, modifications of the Ag(111) SS band structure are shown and quantified, including gap openings and lifts of band degeneracies, driven exclusively by the structural chirality of the 2D MOF phases. These findings highlight how structural symmetries, in particular chirality, affect electronic states at material interfaces, expanding on the toolkit for designing 2D materials with tailored electronic properties.

band structure engineering↗

DOE OSTI2022

Effects of Supplementation in Upper Yakima River Chinook Salmon

Abstract To promote recovery of natural salmonid populations, managers are utilizing hatchery supplementation programs to increase abundance of spawners on the spawning grounds. However, studies have provided evidence that captive breeding can result in domestication, demonstrated by lower fitness of hatchery‐origin compared with natural‐origin fish. Supplementation programs, therefore, typically use natural‐origin broodstock in an effort to minimize long‐term negative fitness impacts. Here we evaluated the upper Yakima River spring supplementation program for Chinook Salmon Oncorhynchus tshawytscha , which has broodstock comprised exclusively of unmarked fish presumed to be of natural‐origin. Using 5 years of spawner data, we tested for effects of hatchery breeding and rearing on total adult returns and their individual reproductive success when spawning naturally. Our study revealed that supplementation increased overall abundance of fish spawning naturally on the spawning grounds. However, on average, compared with natural‐origin spawners, hatchery‐origin fish had reduced reproductive success, which also translated to reduced reproductive success in three out of five return years for natural‐origin fish that spawned with hatchery‐origin fish. As expected, body length and return timing were also significant predictors of reproductive success. However, more generations of data are needed to establish the extent to which reduced reproductive success is passed on to naturally produced progeny.

Koch, Ilana J.↗

DOE OSTI2020

Structure-Composition Subtleties in NaZn 13 -type Derivatives of Sr/Ca(Au x Al 1– x ) 12–13

In the ternary (Sr/Ca)-Au-Al phase space for 5–8 at % Sr/Ca and nearly equimolar mixture of Au and Al, five new NaZn 13 -derivatives Sr/Ca(Au x Al 1–x ) 12–13 were discovered and their atomic site preferences and electronic structures were studied: (1) at higher Au content, cubic SrAuxAl 13–x [7.24(2) ≥ x ≥ 6.68(2)] shows no obvious atomic site preferences; (2) at lower Au content, tetragonal SrAu x Al 13–x [6.59(1) ≥ x ≥ 6.35(3)] shows icosahedra exclusively centered by Al and preferential atomic arrangements to maximize the number of Au–Al (or Al-rich) shortest distances; (3) a monoclinic SrAu 6.10(3) Al 6.40 compound was uncovered from studies of a single crystal specimen with problematic refinement issues but more detailed powder X-ray diffraction analysis which suggest even more pronounced geometric distortion from the NaZn 13 -type structure as well as preferential arrangements for Au–Al nearest contacts; (4) tetragonal SrAu 5.75(2) Al 6.25 with all empty icosahedra; and (5) orthorhombic CaAu 6.09(2) Al 6.01(1) with icosahedra that are half empty and half partially occupied by Al. Electronic DOS and COHP curves were used to rationalize the structural depiction of Sr/Ca(Au x Al 1–x ) 12–13 as icosahedra packing of (Au x Al 1–x) 12–13 with voids filled by the electropositive Sr/Ca.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Exploring Gradient-Based Multi-directional Controls in GANs

Generative Adversarial Networks (GANs) have been widely applied in modeling diverse image distributions. However, despite its impressive applications, the structure of the latent space in GANs largely remains as a black-box, leaving its controllable generation an open problem, especially when spurious correlations between different semantic attributes exist in the image distributions. To address this problem, previous methods typically learn linear directions or individual channels that control semantic attributes in the image space. However, they often suffer from imperfect disentanglement, or are unable to obtain multi-directional controls. Furthermore, in this work, in light of the above challenges, we propose a novel approach that discovers nonlinear controls, which enables multi-directional manipulation as well as effective disentanglement, based on gradient information in the learned GAN latent space. More specifically, we first learn interpolation directions by following the gradients from classification networks trained separately on the attributes, and then navigate the latent space by exclusively controlling channels activated for the target attribute in the learned directions. Empirically, with small training data, our approach is able to gain fine-grained controls over a diverse set of bi-directional and multi-directional attributes, and we showcase its ability to achieve disentanglement significantly better than state-of-the-art methods both qualitatively and quantitatively.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Evidence for Higgs boson decay to a pair of muons

Evidence for Higgs boson decay to a pair of muons is presented. This result combines searches in four exclusive categories targeting the production of the Higgs boson via gluon fusion, via vector boson fusion, in association with a vector boson, and in association with a top quark-antiquark pair. The analysis is performed using proton-proton collision data at $ \sqrt{s} $ = 13 TeV, corresponding to an integrated luminosity of 137 fb$^{−1}$, recorded by the CMS experiment at the CERN LHC. An excess of events over the back- ground expectation is observed in data with a significance of 3.0 standard deviations, where the expectation for the standard model (SM) Higgs boson with mass of 125.38 GeV is 2.5. The combination of this result with that from data recorded at $ \sqrt{s} $ = 7 and 8 TeV, corresponding to integrated luminosities of 5.1 and 19.7 fb$^{−1}$, respectively, increases both the expected and observed significances by 1%. The measured signal strength, relative to the SM prediction, is $ {1.19}_{-0.39}^{+0.40}{\left(\mathrm{stat}\right)}_{-0.14}^{+0.15}\left(\mathrm{syst}\right) $. This result constitutes the first evidence for the decay of the Higgs boson to second generation fermions and is the most precise measurement of the Higgs boson coupling to muons reported to date.[graphic not available: see fulltext]

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

$t\overline{t}t\overline{t}$ signatures through the lens of color-octet scalars

We reinterpret two recent LHC searches for events containing four top quarks ($t\overline{t}t\overline{t}$) in the context of supersymmetric models with Dirac gauginos and color-octet scalars (sgluons). We explore whether sgluon contributions to the four-top production cross section σ ($pp$ → $t\overline{t}t\overline{t}$) can accommodate an excess of four-top events recently reported by the ATLAS collaboration. We also study constraints on these models from an ATLAS search for new phenomena with high jet multiplicity and significant missing transverse energy ($E^{miss}_{T}$) sensitive to signals with four top quarks. We find that these two analyses provide complementary constraints, with the jets + $E^{miss}_{T}$ search exceeding the four-top cross section measurement in sensitivity for sgluons heavier than about 800 GeV. We ultimately find that either a scalar or a pseudoscalar sgluon can currently fit the ATLAS excess in a range of reasonable benchmark scenarios, though a pseudoscalar in minimal Dirac gaugino models is ruled out. We finally offer sensitivity projections for these analyses at the HL-LHC, mapping the 5σ discovery potential in sgluon parameter space and computing exclusion limits at 95% CL in scenarios where no excess is found.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

A theory of dark pions

We present a complete model of a dark QCD sector with light dark pions, broadly motivated by hidden naturalness arguments. The dark quarks couple to the Standard Model via irrelevant Z- and Higgs-portal operators, which encode the low-energy effects of TeV-scale fermions interacting through Yukawa couplings with the Higgs field. The dark pions, depending on their CP properties, behave as either composite axion-like particles (ALPs) mixing with the Z or scalars mixing with the Higgs. The dark pion lifetimes fall naturally in the most interesting region for present and proposed searches for long-lived particles, at the LHC and beyond. This is demonstrated by studying in detail three benchmark scenarios for the symmetries and structure of the theory. Within a coherent framework, we analyze and compare the GeV-scale signatures of flavor-changing meson decays to dark pions, the weak-scale decays of Z and Higgs bosons to hidden hadrons, and the TeV-scale signals of the ultraviolet theory. New constraints are derived from B decays at CMS and from Z-initiated dark showers at LHCb, focusing on the displaced dimuon signature. We also emphasize the strong potential sensitivity of ATLAS and CMS to dark shower signals with large multiplicities and long lifetimes of the dark pions. As a key part of our phenomenological study, we perform a new data-driven calculation of the decays of a light ALP to exclusive hadronic Standard Model final states. The results are provided in a general form, applicable to any model with arbitrary flavor-diagonal couplings of the ALP to fermions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

The Migdal effect in semiconductors for dark matter with masses below ~ 100 MeV

Dark matter scattering off a nucleus has a small probability of inducing an observable ionization through the inelastic excitation of an electron, called the Migdal effect. We use an effective field theory to extend the computation of the Migdal effect in semiconductors to regions of small momentum transfer to the nucleus, where the final state of the nucleus is no longer well described by a plane wave. Our analytical result can be fully quantified by the measurable dynamic structure factor of the semiconductor, which accounts for the vibrational degrees of freedom (phonons) in a crystal. We show that, due to the sum rules obeyed by the structure factor, the inclusive Migdal rate and the shape of the electron recoil spectrum is well captured by approximating the nuclei in the crystal as free ions; however, the exclusive differential rate with respect to energy depositions to the crystal depends on the phonon dynamics encoded in the dynamic structure function of the specific material. Our results now allow the Migdal effect in semiconductors to be evaluated even for the lightest dark matter candidates (m χ ≳ 1 MeV) that can kinematically excite electrons.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Flavor fragmentation function factorization

A definition of partonic jet flavor that is both theoretically well-defined and experimentally robust would have profound implications for measurements and predictions especially for heavy flavor applications. Recently, a definition of jet flavor was introduced as the net flavor flowing along the direction of the Winner-Take-All axis of a jet which is soft safe to all orders, but not collinear safe. Here, we exploit the lack of collinear safety and propose a factorization theorem of perturbative flavor fragmentation functions that resum collinear divergences and describe the evolution of flavor from the short distance of jet production to the long distance at which hadronization occurs. Collinear flavor evolution is governed by a small modification of the DGLAP equations. We present a detailed all-orders analysis and identify exact relations that must hold amongst the various anomalous dimensions by probability conservation and the existence of fixed points of the renormalization group flow. We explicitly validate the factorization theorem at one-loop order, and demonstrate its consistency at two loops in particular flavor channels. Starting at two-loops, constraints on phase space imposed by flavor measurements potentially allow for non-trivial soft contributions, but we demonstrate that they are scaleless and so explicitly vanish, ensuring that soft particles are summed inclusively and all divergences are exclusively collinear in nature. This factorization theorem opens the door to precision calculations with identified flavor in the infrared.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Study of charm hadronization with prompt $ {\Lambda}_{\textrm{c}}^{+} $ baryons in proton-proton and lead-lead collisions at $ \sqrt{s_{\textrm{NN}}} $ = 5.02 TeV

The production of prompt $ {\Lambda}_{\textrm{c}}^{+} $ baryons is measured via the exclusive decay channel $ {\Lambda}_{\textrm{c}}^{+}\to p{\textrm{K}}^{-}{\pi}^{+} $ at a center-of-mass energy per nucleon pair of 5.02 TeV, using proton-proton (pp) and lead-lead (PbPb) collision data collected by the CMS experiment at the CERN LHC. The pp and PbPb data were obtained in 2017 and 2018 with integrated luminosities of 252 and 0.607 nb$^{−1}$, respectively. The measurements are performed within the $ {\Lambda}_{\textrm{c}}^{+} $ rapidity interval |y| < 1 with transverse momentum (p$_{T}$) ranges of 3–30 and 6–40 GeV/c for pp and PbPb collisions, respectively. Compared to the yields in pp collisions scaled by the expected number of nucleon-nucleon interactions, the observed yields of $ {\Lambda}_{\textrm{c}}^{+} $ with p$_{T}$> 10 GeV/c are strongly suppressed in PbPb collisions. The level of suppression depends significantly on the collision centrality. The $ {\Lambda}_{\textrm{c}}^{+} $/D$^{0}$ production ratio is similar in PbPb and pp collisions at p$_{T}$> 10 GeV/c, suggesting that the coalescence process does not play a dominant role in prompt $ {\Lambda}_{\textrm{c}}^{+} $ baryon production at higher p$_{T}$.[graphic not available: see fulltext]

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Search for top squark pair production in a final state with two tau leptons in proton-proton collisions at $ \sqrt{s} =$ 13 TeV

A search for pair production of the supersymmetric partner of the top quark, the top squark, in proton-proton collision events at $ \sqrt{s} $ = 13 TeV is presented in a final state containing hadronically decaying tau leptons and large missing transverse momentum. This final state is highly sensitive to high-tan β or higgsino-like scenarios in which decays of electroweak gauginos to tau leptons are dominant. The search uses a data set corresponding to an integrated luminosity of 77.2 fb$^{−1}$, which was recorded with the CMS detector during 2016 and 2017. No significant excess is observed with respect to the background prediction. Exclusion limits at 95% confidence level are presented in the top squark and lightest neutralino mass plane within the framework of simplified models, in which top squark masses up to 1100 GeV are excluded for a nearly massless neutralino.[graphic not available: see fulltext]

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗