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DOE OSTI2020

Structure of phospholipase Cε reveals an integrated RA1 domain and previously unidentified regulatory elements

Phospholipase Cε (PLCε) generates lipid-derived second messengers at the plasma and perinuclear membranes in the cardiovascular system. It is activated in response to a wide variety of signals, such as those conveyed by Rap1A and Ras, through a mechanism that involves its C-terminal Ras association (RA) domains (RA1 and RA2). However, the complexity and size of PLCε has hindered its structural and functional analysis. Herein, we report the 2.7 Å crystal structure of the minimal fragment of PLCε that retains basal activity. This structure includes the RA1 domain, which forms extensive interactions with other core domains. A conserved amphipathic helix in the autoregulatory X–Y linker of PLCε is also revealed, which we show modulates activity in vitro and in cells. The studies provide the structural framework for the core of this critical cardiovascular enzyme that will allow for a better understanding of its regulation and roles in disease.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Direct observation of entangled electronic-nuclear wave packets

We present momentum resolved covariance measurements of entangled electronic-nuclear wave packets created and probed with octave spanning phaselocked ultrafast pulses. We launch vibrational wave packets on multiple electronic states via multiphoton absorption, and probe these wave packets via strong field double ionization using a second phaselocked pulse. Momentum resolved covariance mapping of the fragment ions highlights the nuclear motion, while measurements of the yield as a function of the relative phase between pump and probe pulses highlight the electronic coherence. The combined measurements allow us to directly visualize the entanglement between the electronic and nuclear degrees of freedom and follow the evolution of the complete wavefunction. Published by the American Physical Society 2024

Moğol, Gönenç↗

DOE OSTI2022

Investigating charm production and fragmentation via azimuthal correlations of prompt D mesons with charged particles in pp collisions at $\mathbf {\sqrt{ s} = 13}$ TeV

Angular correlations of heavy-flavour and charged particles in high-energy proton–proton collisions are sensitive to the production mechanisms of heavy quarks and to their fragmentation as well as hadronisation processes. The measurement of the azimuthal-correlation function of prompt D mesons with charged particles in proton–proton collisions at a centre-of-mass energy of $\sqrt{s} = 13$ TeV with the ALICE detector is reported, considering $\mathrm D^{0} $ , $\mathrm D^{+} $ , and $\mathrm D^{*+} $ mesons in the transverse-momentum interval $3< p_{\mathrm{T}} < 36$ GeV/ $c$ at midrapidity ( $|y| < 0.5$ ), and charged particles with $p_{\mathrm{T}} > 0.3$ GeV/ $c$ and pseudorapidity $|\eta | < 0.8$ . This measurement has an improved precision and provides an extended transverse-momentum coverage compared to previous ALICE measurements at lower energies. The study is also performed as a function of the charged-particle multiplicity, showing no modifications of the correlation function with multiplicity within uncertainties. The properties and the transverse-momentum evolution of the near- and away-side correlation peaks are studied and compared with predictions from various Monte Carlo event generators. Among those considered, PYTHIA8 and POWHEG+PYTHIA8 provide the best description of the measured observables. The obtained results can provide guidance on tuning the generators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Jet fragmentation transverse momentum distributions in pp and p-Pb collisions at $ \sqrt{s}$, $\sqrt{s_{\mathrm{NN}}}$ = 5.02 TeV

Jet fragmentation transverse momentum ( j T ) distributions are measured in proton-proton (pp) and proton-lead (p-Pb) collisions at s NN = 5 . 02 TeV with the ALICE experiment at the LHC. Jets are reconstructed with the ALICE tracking detectors and electromagnetic calorimeter using the anti- k T algorithm with resolution parameter R = 0 . 4 in the pseudorapidity range |η| < 0 . 25. The j T values are calculated for charged particles inside a fixed cone with a radius R = 0 . 4 around the reconstructed jet axis. The measured j T distributions are compared with a variety of parton-shower models. Herwig and P ythia 8 based models describe the data well for the higher j T region, while they underestimate the lower j T region. The j T distributions are further characterised by fitting them with a function composed of an inverse gamma function for higher j T values (called the “wide component”), related to the perturbative component of the fragmentation process, and with a Gaussian for lower j T values (called the “narrow component”), predominantly connected to the hadronisation process. The width of the Gaussian has only a weak dependence on jet transverse momentum, while that of the inverse gamma function increases with increasing jet transverse momentum. For the narrow component, the measured trends are successfully described by all models except for Herwig. For the wide component, Herwig and PYTHIA 8 based models slightly underestimate the data for the higher jet transverse momentum region. These measurements set constraints on models of jet fragmentation and hadronisation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Fragment-based initialization for quantum subspace methods

Here, we present a novel quantum-classical algorithm called LAS-QKSD for multireference systems, by combining a classical localized active space (LAS) fragment-based multireference algorithm with the quantum Krylov subspace diagonalization (QKSD) method for quantum computers. The algorithm uses wave function information from a LAS self-consistent field (LASSCF) calculation to prepare an initial state with better overlap with the target ground state than the Hartree-Fock state. This is coupled with the use of QKSD to ultimately converge to the exact energy, providing faster convergence than starting from the Hartree-Fock state. Fragmentation has the two-fold benefit of fewer configurations on the classical side of the algorithm as well as fewer state preparation gates on the quantum side. First, we compare the LAS-QKSD method to the classical LASSCF method and to QKSD with a Hartree-Fock initial state. We then examine ways to load the LASSCF wave function using direct initialization and a QKSD-motivated spectral filtering approach. Finally, using a bimetallic complex, we show that the LAS-QKSD method is an efficient alternative to highly expensive complete active space SCF (CASSCF) calculations on strongly correlated systems.

D'Cunha, Ruhee↗

DOE OSTI2020

Nucleon localization function in rotating nuclei

An electron localization function was originally introduced to visualize in positional space bond structures in molecules. It became a useful tool to describe electron configurations in atoms, molecules, and solids. In nuclear physics, a nucleon localization function (NLF) has been used to characterize cluster structures in light nuclei, formation of fragments in fission, and pasta phases appearing in the inner crust of neutron stars. In the case of a deformed rotating nucleus, several NLFs can be introduced, depending on the definition of the spin-quantization axis, direction of the total angular momentum, and self-consistent symmetries of the system. Contributions to the NLF from the current density, spin-current tensor density, and density gradient terms are negligible in the nuclear interior. The oscillating pattern of the simplified NLF can be explained in terms of a constructive interference between kinetic-energy and particle densities. The characteristic nodal pattern seen in the NLF in the direction of major axis of a rotating nucleus comes from single-particle orbits carrying large aligned angular momentum. The variation of the NLF along the minor axis of the nucleus can be traced back to deformation-aligned orbits.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Inclusive breakup cross sections in reactions induced by the nuclides 6 He and 6,7 Li in the two-body cluster model

Calculations of inclusive α particle production are performed to interpret reaction experimental data induced by the two-neutron halo 6He and the isotopes 6,7 Li on different target nuclei. In this work, we have implemented the zero-range post-form DWBA to compute the elastic and nonelastic breakup cross sections. Integrated cross sections, angular distributions and spectra are presented. Projectiles are approximated as two-body clusters, namely 6 He as α+dineutron and 6 Li ( 7 Li) are interpreted as α+deuteron(triton). The São Paulo optical potential is employed in the calculation of the distorted wave functions for the incident channels, while standard phenomenological interactions are taken for the fragment-target interactions. Calculations for 6 Li and 7 Li furnish a good description of the data, while the reaction involving 6 He is found to be more complicated, where interpretation of the data must still be considered incomplete. The present analysis identifies an overall large contribution from inclusive breakup emission for all the cases studied.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Multiplicity-dependent jet modification from di-hadron correlations in pp collisions at $ \sqrt{s} $ = 13 TeV

Short-range correlations between charged particles are studied via two-particle angular correlations in pp collisions at $\sqrt{s}$ = 13 TeV. The correlation functions are measured as a function of the relative azimuthal angle ∆φ and the pseudorapidity separation ∆η for pairs of primary charged particles within the pseudorapidity interval |η| < 0.9 and the transverse-momentum range 1 < p T < 8 GeV/c. Near-side (|∆φ| < 1.3) peak widths are extracted from a generalised Gaussian fitted over the correlations in full pseudorapidity separation (|∆η| < 1.8), while the per-trigger associated near-side yields are extracted for the short-range correlations (|∆η| < 1.3). Both are evaluated as a function of charged-particle multiplicity obtained by two different event activity estimators. The width of the near-side peak decreases with increasing multiplicity, and this trend is reproduced qualitatively by the Monte Carlo event generators PYTHIA 8, AMPT, and EPOS. However, the models overestimate the width in the low transverse-momentum region (p T < 3 GeV/c). The per-trigger associated near-side yield increases with increasing multiplicity. Although this trend is also captured qualitatively by the considered event generators, the yield is mostly overestimated by the models in the considered kinematic range. The measurement of the shape and yield of the short-range correlation peak can help us understand the interplay between jet fragmentation and event activity, quantify the narrowing trend of the near-side peak as a function of transverse momentum and multiplicity selections in pp collisions, and search for final-state jet modification in small collision systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Evaluation of Surface Crack Formation in Photovoltaic Backsheets Using Fragmentation and Finite Element Simulations

Backsheet cracking is among the most commonly observed degradation modes of photovoltaic modules in the field. Cracks can reduce the ability of backsheets to fulfill their functions, such as protection of the modules from the environment or electrical insulation. Here, this work presents an evaluation of the degradation and cracking propensity of two backsheets during accelerated IEC TS 62788-7-2 (International Electrotechnical Commission) aging under the A3 condition with a fragmentation test using a coextruded polyamide backsheet (AAA), and a laminated multilayer backsheet with a polyethylene terephthalate core and outer layer and ethylene vinyl acetate inner layer (PPE). Results show the surface embrittlement of the AAA outer layer during exposure. A longer time of exposure causes cracks to form at lower strains during stretching and creates deeper cracks. Accordingly, Young's modulus of the outer layer increases, as measured by cross-sectional nanoindentation. PPE exhibits cracking after exposure as well. While no similar increase of modulus or crack depth can be observed, the outer layer of PPE exhibits more obvious signs of erosion during exposure, including progressive morphological changes and thickness losses. A finite element model is developed to simulate surface crack formation, based on initially zero-thickness decohesion elements. Decohesion criteria define a critical stress, at which these elements grow, and cracks can begin to form. These criteria are obtained via parameter optimization by comparison between simulation and experiment. The model is used to interpret crack formation in both backsheets.

14 SOLAR ENERGY↗

DOE OSTI2024

Atomistic simulations for investigation of substrate and salt effects on lipid in-source fragmentation in secondary ion mass spectrometry: A follow-up study

In-source fragmentation (ISF) poses a significant challenge in secondary ion mass spectrometry (SIMS). These fragment ions increase the spectral complexity and can lead to incorrect annotation of fragments as intact species. The presence of salt that is ubiquitous in biological samples can influence the fragmentation and ionization of analytes in a significant manner, but their influences on SIMS have not been well characterized. To elucidate the effect of substrates and salt on ISF in SIMS, we have employed experimental SIMS in combination with atomistic simulations of a sphingolipid on a gold surface with various NaCl concentrations as a model system. Our results revealed that a combination of bond dissociation energy and binding energy between N-palmitoyl-sphingomyelin and a gold surface is a good predictor of fragment ion intensities in the absence of salt. However, ion-fragment interactions play a significant role in determining fragment yields in the presence of salt. Additionally, the charge distribution on fragment species may be a major contributor to the varying effects of salt on fragmentation. This study demonstrates that atomistic modeling can help predict ionization potential when salts are present, providing insights for more accurate interpretations of complex biological spectra.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Evaluation of Surface Crack Formation in Photovoltaic Backsheets Using Fragmentation and Finite Element Simulations: Preprint

Backsheet cracking is among the most commonly observed degradation modes of photovoltaic (PV) modules in the field. Cracks can reduce the ability of backsheets to fulfil their functions, for example, protection of the modules from the environment or electrical insulation. This work presents an evaluation of the degradation and cracking propensity of two backsheets during accelerated IEC TS 62788-7-2 A3 (International Electrotechnical Commission) aging with the fragmentation test: a co-extruded polyamide backsheet (AAA), and a laminated multilayer backsheet with a polyethylene terephthalate core and outer layer and ethylene vinyl acetate inner layer (PPE). Results show the surface embrittlement of the AAA outer layer during exposure. A longer time of exposure causes cracks to form at lower strains during stretching and creates deeper cracks. Accordingly, Young's modulus of the outer layer increases, as measured by cross-sectional nanoindentation. PPE exhibits cracking after exposure as well. While no similar increase of modulus or crack depth can be observed, the outer layer of PPE exhibits more obvious signs of erosion during exposure, including progressive morphological changes and thickness losses. A finite element model to simulate surface crack formation is devised, based on initially zero-thickness decohesion elements. Decohesion criteria define a critical stress, at which these elements grow, and cracks can begin to form. These criteria are obtained via parameter optimization by comparison between simulation and experiment. The model is used to interpret crack formation in both backsheets.

backsheet↗

DOE OSTI2026

Conservation laws and effective hadronization models

Hadronization models based on local string-breaking dynamics are typically Markovian by construction, yet the physical ensemble of final states is shaped by global constraints that couple the entire fragmentation trajectory. Recasting hadronization as a conditioned stochastic diffusion process provides a precise mathematical resolution to this tension. In particular, this language reveals explicitly that constraints stemming from conservation laws induce non-Markovian correlations between otherwise independent fragmentation steps, and that these correlations can be absorbed exactly into a renormalization of the local dynamics through a Doob $h$-transform. We develop this formalism for a $q\bar{q}$ string in the chiral limit, where the longitudinal-transverse factorization of the Lund kernel becomes exact, enabling systematic power counting and clean ultraviolet (UV)/infrared (IR) separation. The dynamics organize naturally into a tower of effective theories distinguished by the remaining string mass, spanning a UV fixed point with scale-invariant transport coefficients, an intermediate regime where transverse phase space induces controlled running, and an IR boundary layer where non-local effects enter at leading order. The tower exhibits genuine Wilsonian structure, including $β$-functions, anomalous dimensions, and systematic matching conditions. The resulting framework achieves a clean factorization of universal microscopic fragmentation dynamics from infrared constraint effects, and opens new directions for both the theoretical analysis and practical simulation of hadronization.

Menzo, Tony [Alabama U.; Fermilab] (ORCID:00000002↗

DOE OSTI2024

Disturbance and diversity: Lichen species richness decreases with increasing anthropogenic disturbance

Anthropogenic disturbance is rapidly increasing through habitat degradation, development, and deforestation. Gaps remain in understanding the effects of this disturbance on diverse and ecologically important organisms such as lichens. In North America, studies have focused on epiphytic macrolichens and catastrophic disturbance, largely ignoring microlichens and less severe disturbances. The Intermediate Disturbance Hypothesis predicts these moderate disturbances will lead to higher species richness. Here we examine the effects of anthropogenic disturbance in the form of land management on overall lichen richness, including microlichens, and on the species richness of eight lichen functional groups. The study draws on a comprehensive data set of 872 species, in 208 one-hectare plots throughout the Southern Appalachian Mountains, a global biodiversity hotspot in eastern North America. A habitat quality index based on an established forestry metric was used as a proxy for anthropogenic disturbance and was quantified using a 10-part score including categories such as percent native tree canopy cover and degree of fragmentation. Linear models were used to compare habitat quality scores to overall species richness and to species richness of functional groups. Rather than following the Intermediate Disturbance Hypothesis, all groups uniformly follow a negative linear relationship: as disturbance increases, species richness decreases. This pattern held even for widely variable functional groups such as morphotype. Effective conservation of lichen richness should prioritize the maintenance of existing older, less-disturbed stands within large, contiguously forested areas.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Well-Tunable, 3D-printable, and Fast Autonomous Self-Healing Elastomers

Self-healing elastomers provide extended longevity of functional materials, due to their unique adaptability and durability. However, a major scientific challenge remains in developing materials with a rapid healing process combined with decent mechanical properties, that can be prepared by a relatively simple synthesis approach. Herein, we report a versatile design approach on self-healing elastomers by incorporating two different hydrogen bonding containing monomers, i.e., 2-[[(butylamino)carbonyl]oxy]ethyl acrylate (BCOE) and 2-ureido-4[1H]pyrimidinone (UPy) functionalized ethyl methacrylate. Poly(BCOE-r-UPy)s are synthesized by reversible addition-fragmentation chain-transfer (RAFT) polymerization, and controlling the ratio of two monomers enables well-tunable mechanical properties with tensile strength ranging from 0.04 to 6.3 MPa and tensile strain up to 3,000 %. The characteristic dissociation energy is calculated from a temperature dependence of terminal relaxation followed by subtracting the segmental relaxation. The rapid autonomous self-healing is achieved when the molar composition of Poly(BCOE-r-UPy) is tailored to BCOE/UPy = 99/1. The self-healing process is monitored in situ by a helium-ion microscope, and its macroscopic study using tensile tests indicates that Poly(BCOE-r-UPy1) with 1 % molar ratio of UPy recovers 70 % of its original toughness at ambient temperature within 10 mins. 3D printing of Poly(BCOE-r-UPy) affords a self-healable 3D structure, demonstrating the adaptability of Poly(BCOE-r-UPy) for on-demand fabrication. The simplicity of synthesis, well-tunable mechanical properties, unique self-healability, and 3D printing capability of Poly(BCOE-r-UPy)s indicate their potential for a range of applications.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Field-Coupled Water Splitting with Metal-Free Donor–Acceptor Covalent Organic-Framework Junctions

Advancing metal-free electrocatalysts for hydrogen and oxygen evolution reactions (HER/OER) across acidic and alkaline media requires coordinated control of intermediate binding thermodynamics, interfacial charge delivery, and near-electrode transport dynamics. Here, we design amide-linked benzene–triazine covalent organic frameworks (BTA/TzTA-Hz COFs) and integrate them with carbon nanotubes (CNTs) to form COF–CNT junctions that establish a built-in interfacial electric field. Density functional theory (DFT) and electrostatic potential maps indicate complementary active motifs, with benzene-proximal fragments associated with HER and triazine-proximal motifs associated with OER. CNT integration shifts the contact-potential difference by ≈0.20 V, while operando electrochemical impedance spectroscopy suggests partially separable high-frequency junction-charging and lower-frequency Faradaic/transport responses. A 300 mT static magnetic field lowers the HER and OER overpotentials by tens of millivolts. Under anodic bias, the effective interfacial charging capacitance increases, and Mott–Schottky analysis shows an apparent ∼0.15 V flat-band shift with an essentially unchanged slope. Together, these observations are consistent with field-perturbed interfacial charging and altered bias partitioning. Field-dependent impedance and bubble imaging are consistent with magnetohydrodynamic convection that promotes bubble detachment and near-electrode mass transport for both half-reactions, and they reveal an OER-specific high-frequency perturbation under anodic bias. Under field, the heterostructure reaches an OER onset overpotential of ∼261 mV and requires an overpotential of 366 mV at 10 mA cm –2 in alkaline electrolyte. These results illustrate how reticular-framework chemistry, junction engineering, and both built-in and applied fields can program reactivity through interfacial electrostatics and near-electrode transport in organic-framework electrocatalysts.

Garcia-Enriquez, Lissette [Univ. of Texas at El Pa↗

DOE OSTI2024

PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data

Mass spectrometry is broadly employed to study complex molecular mechanisms in various biological and environmental fields, enabling 'omics' research such as proteomics, metabolomics, and lipidomics. As study cohorts grow larger and more complex with dozens to hundreds of samples, the need for robust quality control (QC) measures through automated software tools becomes paramount to ensure the integrity, high quality, and validity of scientific conclusions from downstream analyses and minimize the waste of resources. Since existing QC tools are mostly dedicated to proteomics, automated solutions supporting metabolomics are needed. To address this need, we developed the software PeakQC, a tool for automated QC of MS data that is independent of omics molecular types (i.e., omics-agnostic). It allows automated extraction and inspection of peak metrics of precursor ions (e.g., errors in mass, retention time, arrival time) and supports various instrumentations and acquisition types, from infusion experiments or using liquid chromatography and/or ion mobility spectrometry front-end separations and with/without fragmentation spectra from data-dependent or independent acquisition analyses. Diagnostic plots for fragmentation spectra are also generated. Here, in this paper, we describe and illustrate PeakQC’s functionalities using different representative data sets, demonstrating its utility as a valuable tool for enhancing the quality and reliability of omics mass spectrometry analyses.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Investigating the broadening phenomenon in two-particle correlations induced by gluon saturation

It has been found that the gluon density inside the proton grows rapidly at small momentum fractions. Quantum chromodynamics (QCD) predicts that this growth can be regulated by nonlinear effects, ultimately leading to gluon saturation. Within the color glass condensate framework, nonlinear QCD effects are predicted to suppress and broaden back-to-back angular correlations in collisions involving heavy nuclei. While suppression has been observed in various experiments in 𝑑/𝑝 + A collisions compared to 𝑝 + 𝑝 collisions, the predicted broadening remains unobserved. This study investigates the contributions of intrinsic transverse momentum (𝑘 𝑇 ), which is associated with saturation physics, as well as parton showers and transverse motion from fragmentation (𝑝$^{frag}_{𝑇}$), which are not saturation dependent, to the width of the correlation function. Our findings show that the non-saturation dependent effects, especially the initial-state parton shower and 𝑝$^{frag}_{𝑇}$, which occur independently of the collision system, smear the back-to-back correlation more than gluon saturation does, making the broadening phenomenon difficult to observe.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

A genetic toolbox for metabolic engineering of Issatchenkia orientalis

The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. Yet, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis, which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As evidence of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis.

59 BASIC BIOLOGICAL SCIENCES↗