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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Stabilization of a Heme-HNO Model Complex Using a Bulky Bis-Picket Fence Porphyrin and Reactivity Studies with NO

Nitroxyl, HNO/NO – , the one-electron reduced form of NO, is suggested to take part in distinct signaling pathways in mammals and is also a key intermediate in various heme-catalyzed NO x interconversions in the nitrogen cycle. Cytochrome P450nor (Cyt P450nor) is a heme-containing enzyme that performs NO reduction to N 2 O in fungal denitrification. The reactive intermediate in this enzyme, termed “Intermediate I”, is proposed to be an Fe-NHO/Fe-NHOH type species, but it is difficult to study its electronic structure and exact protonation state due to its instability. Here, we utilize a bulky bis-picket fence porphyrin to obtain the first stable heme-HNO model complex, [Fe(3,5-Me-BAFP)(MI)(NHO)], as a model for Intermediate I, and more generally HNO adducts of heme proteins. Due to the steric hindrance of the bis-picket fence porphyrin, [Fe(3,5-Me-BAFP)(MI)(NHO)] is stable (τ 1/2 = 56 min at -30 °C), can be isolated as a solid, and is available for thorough spectroscopic characterization. In particular, we were able to solve a conundrum in the literature and provide the first full vibrational characterization of a heme-HNO complex using IR and nuclear resonance vibrational spectroscopy (NRVS). Reactivity studies of [Fe(3,5-Me-BAFP)(MI)(NHO)] with NO gas show a 91 ± 10% yield for N 2 O formation, demonstrating that heme-HNO complexes are catalytically competent intermediates for NO reduction to N 2 O in Cyt P450nor. In conclusion, the implications of these results for the mechanism of Cyt P450nor are further discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP

YiiP is a secondary transporter that couples Zn 2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn 2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn 2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn 2+ . To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn 2+ and validated its performance with known Zn 2+ -binding proteins. Using these tools, we find that, in the presence of Zn 2+ , YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn 2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn 2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn 2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The PDF4LHC21 combination of global PDF fits for the LHC Run III

A precise knowledge of the quark and gluon structure of the proton, encoded by the parton distribution functions (PDFs), is of paramount importance for the interpretation of high-energy processes at present and future lepton–hadron and hadron–hadron colliders. Motivated by recent progress in the PDF determinations carried out by the CT, MSHT, and NNPDF groups, we present an updated combination of global PDF fits: PDF4LHC21. It is based on the Monte Carlo combination of the CT18, MSHT20, and NNPDF3.1 sets followed by either its Hessian reduction or its replica compression. Extensive benchmark studies are carried out in order to disentangle the origin of the differences between the three global PDF sets. In particular, dedicated fits based on almost identical theory settings and input datasets are performed by the three groups, highlighting the role played by the respective fitting methodologies. We compare the new PDF4LHC21 combination with its predecessor, PDF4LHC15, demonstrating their good overall consistency and a modest reduction of PDF uncertainties for key LHC processes such as electroweak gauge boson production and Higgs boson production in gluon fusion. We study the phenomenological implications of PDF4LHC21 for a representative selection of inclusive, fiducial, and differential cross sections at the LHC. The PDF4LHC21 combination is made available via the LHAPDF library and provides a robust, user-friendly, and efficient method to estimate the PDF uncertainties associated to theoretical calculations for the upcoming Run III of the LHC and beyond.

quantum chromodynamics↗
DOE OSTI2022

Thermonuclear reaction rate of 29 Si(p,γ) 30 P

The thermonuclear rate of the 29 Si(p,γ) 30 P reaction impacts the 29 Si abundance in classical novae. A reliable reaction rate is essential for testing the nova paternity of presolar stardust grains. At present, the fact that no classical nova grains have been unambiguously identified in primitive meteorites among thousands of grains studied is puzzling, considering that classical novae are expected to be prolific producers of dust grains. We investigated the 29 Si + p reaction at center-of-mass energies of 200–420 keV, and present improved values for resonance energies, level excitation energies, resonance strengths, and branching ratios. One new resonance was found at a center-of-mass energy of 303 keV. For an expected resonance at 215 keV, an experimental upper limit could be determined for the strength. We evaluated the level structure near the proton threshold, and present new reaction rates based on all the available experimental information. Our new reaction rates have much reduced uncertainties compared with previous results at temperatures of T ≥ 140 MK, which are most important for classical nova nucleosynthesis. Furthermore, future experiments to improve the reaction rates at lower temperatures are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Inclusive and exclusive electron scattering data analysis from Jefferson Lab experiment E12-14-012

Since the first observations of neutrino oscillation, neutrino experiments have come a long way toward precise measurements of the neutrino oscillation parameters, but some obstacles still remain. The next generation of oscillation experiments, including the Deep Underground Neutrino Experiment (DUNE), will be using the Liquid Argon Time Projection Chambers (LArTPCs) with natural argon as the neutrino target material. A precise model of the neutrino cross section on argon does not exist, which is a source of significant uncertainty in such experiments. The E12-14-012 experiment at Jefferson Lab seeks to help remedy this via electron scattering measurements on argon and titanium targets. The experiment collected both inclusive (e,e') and exclusive (e,e'p) data at a wide range of kinematics with the intent to measure the electron-nucleus cross section and thus derive a spectral function for argon that can be used with neutrino experiments. The use of titanium in this experiment stems from the equivalent shell structure that its protons share with the neutrons in argon, which will be crucial in oscillation experiments but cannot be measured directly in electron scattering. This thesis collects several papers which present results from the E12-14-012 experiment. These results include the inclusive (e,e') cross sections for carbon, titanium, argon, and aluminum at a beam energy of 2.22 GeV and a scattering angle of 15.54 deg with uncertainty of less than 5%. Also included are the first results of the exclusive (e,e'p) cross section on argon and titanium.

Murphy, Matthew D.↗
DOE OSTI2025

Proton Spin from Small-x With Constraints from the Valence Quark Model

We apply the valence quark model to constrain the non-perturbative initial condition for the small-x helicity evolution. The remaining free parameters are constrained by performing a global analysis to the available polarized small-x deep inelastic scattering data. A good description of the world data is obtained with only 8 free parameters. The model parameters are tightly constrained by the data, allowing us to predict the proton polarized structure-function to be negative at small x. Furthermore, we obtain the small-x quark and gluon spins, depending on the applied running coupling prescription.

Adamiak, Daniel [Thomas Jefferson National Acceler↗
DOE OSTI2024

Threshold charmonium photoproduction with GlueX

We report the total and differential cross sections for J/ψ photoproduction obtained using the large acceptance GlueX spectrometer at the 12 GeV JLab accelerator over the full near-threshold kinematic region. The GlueX experiment uses tagged linearly-polarized photon beam from coherent Bremsstrahlung off a thin diamond. Charmonium photoproduction near threshold, under certain assumptions including gluon exchange and factorization, can be used to study important aspects of the gluon structure of the proton, such as the gluon GPD, the gravitational form factors, the mass radius of the proton, and the anomalous contribution to the proton mass. In the measured cross sections we find evidence for possible contributions beyond gluon exchange. The results are compared to a wide range of theoretical predictions including GPD calculations and models with open-charm intermediate states. Photoproduction near threshold of charmonium states with opposite-to-photon parity offer another opportunity, complementary to the J/ψ, to understand the reaction mechanism of the charmonium photoproduction. While we see some evidence for such states, comprehensive studies of such higher-mass charmonia can be done only with the proposed JLab energy upgrade. An electron beam energy of up to 22 GeV significantly increases the photon flux and polarization in the corresponding threshold regions allowing for precise cross section and polarization measurements there.

Pentchev, Lubomir↗
DOE OSTI2021

J/Psi Photoproduction Near Threshold With CLAS12

The structure of the proton is comprised of quarks and a sea of gluons. A mechanism that can extract the characteristics of the hidden-color correlations of the nuclear wavefunction is the production of charm near threshold. Due to the fact that momentum transfer is large near threshold in the production of J/ψ , all three valence quarks must act coherently to ex- change energy for the reaction to occur. Models have been developed to predict the nature of J/ψ photoproduction at these specific energies. These include production mechanisms with the two-gluon and three-gluon exchanges. The transferred momentum dependence of the differential cross sections are sensitive to the gluonic form factors, which describe the distribution of color charge in the proton. The CLAS12 detector is capable of measuring J/ψ photoproduction at the energy range close to the threshold. Work showcased in this dissertation encompasses the preparation of the CLAS12 experiments, including the optimization of tracking reconstruction through the study of the Torus magnetic field. In terms of software, contributions were made to the CLAS12 Event Builder, a key stage of reconstruction where event-by-event information is summarized for efficient data analysis. After the run periods were successfully completed, analysis of the RG-A data commenced and an analysis framework was developed to measure the differential and total cross sections of J/ψ photoproduction in Hall B.

Newton, Joseph↗
NASA NTRS1979

Predictions of induced background radiations at gamma/X-ray experiment envelopes in NASA spacecraft

This work seeks to predict secondary radiation levels induced in spacecraft structures by space protons. The radiations analyzed are secondary neutrons from spallation and evaporation reactions and gamma and beta rays from the decay of induced radioactivity, as sources of interfering background to spaceborne measurements of galactic and planetary gamma rays below 10 MeV. The spacecraft considered are the Multi-Mission Spacecraft (MMS) and the Space Shuttle, modeled as spherical shells. The proton environment is that of the South Atlantic Anomaly, as well as cosmic ray protons. The induced radioactivity is analyzed in terms of its interference with various gamma-ray lines of astrophysical interest, as well as its contribution to several spectral regions of the gamma-ray continuum. The buildup of the line and continuum radioactivity background is predicted for a period of nearly 9 months in orbit (approximately 4100 orbits). In addition, background contributions from cosmic ray electron bremsstrahlung and earth gamma-ray albedo are estimated.

Fischbein, W. L.↗
NASA NTRS2012

Metasomatic Control of Water in Garnet and Pyroxene from Kaapvaal Craton Mantle Xenoliths

Fourier transform infrared spectrometry (FTIR) and laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) were used to determine water, rare earth (REE), lithophile (LILE), and high field strength (HFSE) element contents in garnet and pyroxene from mantle xenoliths, Kaapvaal craton, southern Africa. Water enters these nominally anhydrous minerals as protons bonded to structural oxygen in lattice defects. Pyroxene water contents (150-400 ppm in clinopyroxene; 40-250 ppm in orthopyroxene) correlate with their Al, Fe, Ca and Na and are homogeneous within a mineral grains and a xenolith. Garnets from Jagersfontein are chemically zoned for Cr, Ca, Ti and water contents. Garnets contain 0 to 20 ppm H2 Despite the fast diffusion rate of H in mantle m inerals, the observations above indicate that the water contents of mantle xenolith minerals were not disturbed during kimberlite entrainment and that the measured water data represent mantle values. Trace elements in all minerals show various degrees of light REE and LILE enrichments indicative of minimal to strong metasomatism. Water contents of peridotite minerals from the Kaapvaal lithosphere are not related to the degree of depletion of the peridotites. Instead, metasomatism exerts a clear control on the amount of water of mantle minerals. Xenoliths from each location record specific types of metasomatism with different outcomes for the water contents of mantle minerals. At pressures . 5.5 GPa, highly alkaline melts metasomatized Liqhobong and Kimberley peridotites, and increased the water contents of their olivine, pyroxenes and garnet. At higher pressures, the circulation of ultramafic melts reacting with peridotite resulted in co-variation of Ca, Ti and water at the edge of garnets at Jagersfontein, overall decreasing their water content, and lowered the water content of olivines at Finsch Mine. The calculated water content of these melts varies depending on whether the water content of the peridotite (2 wt% HO. 2O) or individual m inerals (<0.5-13 wt% H2O) are used, and also depend on the mineral-melt water partition coefficients. These metasomatic events are thought to have occurred during the Archean and Proterozoic, meaning that the water contents measured here have been preserved since that time and can be used to investigate viscocity and longevity of cratonic mantle roots.

Peslier, Anne H.↗
NASA NTRS2012

Water in Pyroxene and Olivine from Martian Meteorites

Water in the interior of terrestrial planets can be dissolved in fluids or melts and hydrous phases, but can also be locked as protons attached to structural oxygen in lattice defects in nominally anhydrous minerals (NAM) like olivine, pyroxene, or feldspar [1-3]. Although these minerals contain only tens to hundreds of ppm H2O, this water can amount to at least one ocean in mass when added at planetary scales because of the modal dominance of NAM in the mantle and crust [4]. Moreover these trace amounts of water can have drastic effects on melting temperature, rheology, electrical and heat conductivity, and seismic wave attenuation [5]. There is presently a debate on how much water is present in the martian mantle. Secondary ionization mass spectrometry (SIMS) studies of NAM [6], amphiboles and glass in melt inclusions [7-10], and apatites [11, 12] from Martian meteorites report finding as much water as in the same phases from Earth's igneous rocks. Most martian hydrous minerals, however, generally have the relevant sites filled with Cl and F instead of H [13, 14], and experiments using Cl [15] in parent melts can reproduce Martian basalt compositions as well as those with water [16]. We are in the process of analyzing Martian meteorite minerals by Fourier transform infrared spectrometry (FTIR) in order to constrain the role of water in this planet s formation and magmatic evolution

Peslier, A. H.↗
NASA NTRS2013

Water in Nominally Anhydrous Minerals from Nakhlites and Shergottites

Estimating the amount of water in the interior of terrestrial planets has tremendous implications on our understanding of solar nebula evolution, planet formation and geological history, and extraterrestrial volcanism. Mars has been a recent focus of such enquiry with complementary datasets from spacecrafts, rovers and martian meteorite studies. In planetary interiors, water can be dissolved in fluids or melts and hydrous phases, but can also be locked as protons attached to structural oxygen in lattice defects in nominally anhydrous minerals (NAM) such as olivine, pyroxene, or feldspar [1-3]. Measuring water in Martian meteorite NAM is challenging because the minerals are fragile and riddled with fractures from impact processes that makes them break apart during sample processing. Moreover, curing the sample in epoxy causes problems for the two main water analysis techniques, Fourier transform infrared spectrometry (FTIR) and secondary ionization mass spectrometry (SIMS). Measurements to date have resulted in a heated debate on how much water the mantle of Mars contains. SIMS studies of NAM [4], amphiboles [5], and apatites [6-8] from Martian meteorites report finding enough water in these phases to infer that the martian mantle is as hydrous as that of the Earth. On the other hand, a SIMS study of glass in olivine melt inclusions from shergottites concludes that the Martian mantle is much drier [9]. The latter interpretation is also supported by the fact that most martian hydrous minerals generally have the relevant sites filled with Cl and F instead of H [10,11]. As for experimental results, martian basalt compositions can be reproduced using water as well as Cl in the parent melts [12,13]. Here FTIR is used to measure water in martian meteorite minerals in order to constrain the origin of the distribution of water in martian meteorite phases.

Peslier, Anne H.↗
DOE OSTI2024

Gas permeable fluoropolymers and ionomers

Novel copolymers that are fluoropolymers including a first repeat unit that is fluorinated and cyclic and a second repeat unit from a trifluorovinyl methylene ether monomer having sulfur or sulfone functionality in the pendant group are disclosed. The copolymers have relatively high gas permeability as a result of a cyclic repeat unit in the copolymer backbone and ionomers from oxidation of the sulfur containing functionality are particularity useful in the cathode structure of a proton exchange membrane fuel cell.

Lousenberg, Robert Daniel↗
DOE OSTI2026

Probing the flavour structure of dimension-6 EFT operators in multilepton final states in proton-proton collisions at $\sqrt{s}=13$ TeV

An analysis of the flavour structure of dimension-6 effective field theory (EFT) operators in multilepton final states is presented, focusing on the interactions of quarks with Z bosons. For the first time, the flavour structure of these operators is disentangled by simultaneously probing the interactions with different quark generations. The analysis targets the associated production of a top quark pair and a Z boson, as well as diboson processes in final states with at least three leptons, which can be electrons or muons. The data were recorded by the CMS experiment in the years 2016–2018 in proton-proton collisions at a centre-of-mass energy of 13 TeV and correspond to an integrated luminosity of 138 fb −1 . Consistency with the standard model of particle physics is observed and limits are set on the selected Wilson coefficients, split into couplings to light- and heavy-quark generations.

Flavour Physics↗
NASA NTRS2012

Simulations of Magnetic Reconnection - Kinetic Mechanisms Underlying the Fluid Description of Ions

Because of its ability to transfer the energy stored in magnetic field together with the breaking of the flux freezing constraint, magnetic reconnection is considered as one of the most important phenomena in plasma physics. When it happens in a collision less environment such as the terrestrial magnetosphere, it should a priori be modelled with in the framework of kinetic physics. The evidence of kinetic features has incidentally for a long time, been shown by researchers with the help of both numerical simulations and satellite observations. However, most of our understanding of the process comes from the more intuitive fluid interpretation with simple closure hypothesis which do not include kinetic effects. To what extent are these two separate descriptions of the same phenomenon related? What is the role of kinetic effects in the averaged/fluid dynamics of reconnection? This thesis addresses these questions for the proton population in the particular case of anti parallel merging with the help of 2D Hybrid simulations. We show that one can not assume, as is usually done, that the acceleration of the proton flow is only due to the Laplace force. Our results show, for symmetric and asymmetric connection, the importance of the pressure force, opposed to the electric one on the separatrices, in the decoupling region. In the symmetric case, we emphasize the kinetic origin of this force by analyzing the proton distribution functions and explain their structure by studying the underlying particle dynamics. Protons, as individual particles, are shown to bounce in the electric potential well created by the Hall effect. The spatial divergence of this well results in a mixing in phase space responsible for the observed structure of the pressure tensor. A detailed energy budget analysis confirms the role of the pressure force for the acceleration; but, contrary to what is sometimes assumed, it also reveals that the major part of the incoming Poynting flux is transferred to the thermal energy flux rather than to the convective kinetic energy flux, although the latter is generally supposed dominant. In the symmetric case, we propose the pressure tensor to be an additional proxy of the ion decoupling region in satellite data and verify this suggestion by studying a reconnection event encountered by the Cluster spacecrafts. Finally, the last part of this thesis is devoted to the study of the kinetic structure of asymmetric tangential current sheets where connection can develop. This theoretical part consists in finding a steady state solution to the Vlasov-Maxwell system for the protons in such a configuration. We present the theory and its first confrontation to numerical tests.

Aunai, icolas↗
NASA NTRS1979

Coronal magnetic structure and the latitude and longitude distribution of energetic particles, 1-5 AU

The relation of the coronal magnetic field structure to the distribution of approximately 1 MeV protons in interplanetary space between 1 and 5 AU is discussed. After ordering the interplanetary data by its estimated coronal emission source location in heliographic coordinates, the multispacecraft measured proton fluxes are compared with coronal magnetic field structure infrared as observed in soft X-ray photographs and potential field calculations. Evidence for the propagation and possible acceleration of solar flare protons on high magnetic loop structure in the corona is presented. Further, it is shown that corotating proton flux enhancements are associated with regions of low coronal X-ray emission (including coronal holes), usually in association with solar wind stream structure.

Roelof, E. C.↗
DOE OSTI2026

pH-Driven Restructuring of Hydration Layers and Cation Adsorption at the Alumina–Water Interface

Oxide−water interfaces underpin ion separations, catalysis, and electrochemical energy technologies, where the electrical double layer (EDL) controls adsorption, transport, and reactivity. However, the molecular-scale links between pHdependent surface protonation, hydration-layer structure, and counterion adsorption remain poorly defined. Here, we combine in situ crystal truncation rod (CTR) and resonant anomalous X-ray reflectivity (RAXR) with streaming potential measurements and ab initio molecular dynamics (AIMD) simulations to resolve the chemical and structural evolution of the EDL at the single-crystal alumina (012)−water interface in 10 mM Rb + over pH 3−12. CTR measurements reveal two distinct adsorbed water layers at ∼2.2 and ∼3.5 Å above the surface. Each water layer shifts toward the substrate at transition pHs near 6.5 and 10.6, respectively, reflecting changes in primary hydration layer structure in response to the deprotonation of bridging and terminal aluminol groups. RAXR shows a 10-fold increase in Rb + coverage and a decrease in mean adsorption height from ∼3.5 to ∼2.7 Å with increasing pH, indicating enhanced counterion binding accompanied by Stern layer contraction. Streaming potential measurements demonstrate that the zeta potential, i.e., the potential at the hydrodynamic shear plane, is positive at pH 3 and becomes negative at pH ≥ 3.5. The negative charge magnitude increases with increasing pH, consistent with progressive surface deprotonation at higher pH. AIMD identifies inner- and outer-sphere Rb+ complexes whose adsorption heights and coordination geometries depend sensitively on the protonation state of surface oxygens, providing atomistic support for the experimentally inferred trends. These measurements establish two discrete, site-specific pH transitions in hydration-layer structure that track aluminol (de)protonation and quantitatively link them to a pH-driven contraction of the Stern layer (increasing Rb + coverage and decreasing adsorption height). This provides a direct structural basis for connecting surface acid−base chemistry to ion binding distances at an oxide−water interface.

Adsorption↗
DOE OSTI2026

pH-Driven Restructuring of Hydration Layers and Cation Ad-sorption at the Alumina-Water Interface

Oxide-water interfaces underpin ion separation, catalysis, and electrochemical energy technologies, where the electrical double layer (EDL) controls adsorption, transport, and reactivity. Yet, the molecular-scale link between pH-dependent surface protonation, hydration-layer structure, and counter-ion adsorption remains poorly defined. Here, we combine in situ crystal truncation rod (CTR) and resonant anomalous X-ray reflectivity (RAXR) with streaming potential measurements and ab initio molecular dynamics (AIMD) simulations to resolve the chemical and structural evolution of the EDL at the single-crystal alumina (012)-water interface in 10 mM Rb+ over pH 3-12. CTR measurements reveal two distinct adsorbed water layers at ~2.2 and ~3.5 Å above the surface that each shift toward the substrate at transition pHs near 6.5 and 10.6, respectively, directly reflecting changes in primary hydration layer structure in response to the deprotonation of bridging and terminal aluminol groups. RAXR shows a 10-fold increase in Rb+ coverage and a decrease in mean adsorption height from ~3.5 to ~2.7 Å with increasing pH, indicating enhanced counter-ion binding accompanied by Stern layer contraction. Streaming potential measurements demonstrate that the zeta potential, i.e., potential at the hydrodynamic shear plane, is positive at pH 3 and becomes negative at pH ≥3.5. This negative charge magnitude increases with increasing pH, consistent with progressive surface deprotonation at higher pH. AIMD identifies inner- and outer-sphere Rb+ complexes whose adsorption heights and coordination geometries depend sensitively on the protonation state of surface oxygens, providing atomistic support for the experimentally inferred trends. These measurements establish two discrete, site-specific pH transitions in hydration-layer structure that track aluminol (de)protonation and quantitatively link them to a pH-driven contraction of the Stern layer (increasing Rb+ coverage and decreasing adsorption height). This provides a direct structural basis for connecting surface acid-base chemistry to ion binding distances at an oxide-water interface.

Electrical double layer (EDL), Surface protonation↗