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All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Spectral form factors and late time quantum chaos

This is a collection of notes about spectral form factors of standard ensembles in random matrix theory, written for the practical usage of the current study of late time quantum chaos. More precisely, we consider the Gaussian unitary ensemble, the Gaussian orthogonal ensemble, the Gaussian symplectic ensemble, the Wishart-Laguerre unitary ensemble, the Wishart-Laguerre orthogonal ensemble, and the Wishart-Laguerre symplectic ensemble. These results and their physics applications cover a threefold classification of late time quantum chaos in terms of spectral form factors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Nucleon-to-Roper electromagnetic transition form factors at large Q 2

High-precision nucleon-resonance electroproduction data on a large kinematic domain of energy and momentum transfer have proven crucial in revealing novel features of strong interactions within the Standard Model and unfolding structural details of baryon excited states. Thus, in anticipation of new data reaching to unprecedented photon virtuality, we employ a quark-diquark approximation to the three-valence-quark bound-state problem to compute γ*p → R + and γ*n → R 0 transition form factors on Q 2 /m 2 N ϵ[0,12], where m N is the nucleon mass. Having simultaneously analyzed both charged and neutral channels, we also provide a quark-flavor separation of the transition form factors. Furthermore, the results should be useful in planning new-generation experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2013

Charge form factor and sum rules of electromagnetic response functions in $^{12}$C

An {\it ab initio} calculation of the $^{12}$C elastic form factor, and sum rules of longitudinal and transverse response functions measured in inclusive (e,e') scattering, is reported, based on realistic nuclear potentials and electromagnetic currents. The longitudinal elastic form factor and sum rule are found to be in satisfactory agreement with available experimental data. A direct comparison between theory and experiment is difficult for the transverse sum rule. However, it is shown that the calculated one has large contributions from two-body currents, indicating that these mechanisms lead to a significant enhancement of the quasi-elastic transverse response. This fact may have implications for the anomaly observed in recent neutrino quasi-elastic charge-changing scattering data off $^{12}$C.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Tokamak Operation with Safety Factor q 95 < 2 via Control of MHD Stability

Magnetic feedback control of the resistive-wall mode has enabled DIII-D to access stable operation at safety factor q95 = 1:9 in divertor plasmas for 150 instability growth times. Magnetohydrodynamic stability sets a hard, disruptive limit on the minimum edge safety factor achievable in a tokamak, or on the maximum plasma current at given toroidal magnetic eld. In tokamaks with a divertor, the limit occurs at q95 = 2, as con rmed in DIII-D. Since the energy con cement time scales linearly with current, this also bounds the performance of a fusion reactor. DIII-D has overcome this limit, opening a whole new high-current regime not accessible before. This result brings signi cant possible bene ts in terms of fusion performance, but it also extends resistive wall mode physics and its control to conditions never explored before. In present experiments, q95 < 2 operation is eventually halted by voltage limits reached in the feedback power supplies, not by intrinsic physics issues. Improvements to power supplies and to control algorithms have the potential to further extend this regime.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Factorized power expansion for high- p T heavy quarkonium production

In this study, we show that when the factorized cross section for heavy quarkonium production includes next-to-leading power contributions associated with the production of the heavy quark pair at short distances, it naturally reproduces all high p T results calculated in nonrelativistic QCD (NRQCD) factorization. This extended formalism requires fragmentation functions for heavy quark pairs, as well as for light partons. When these fragmentation functions are themselves calculated using NRQCD, we find that two of the four leading NRQCD production channels, ³S [1] 1 and ¹S [8] 0 , are dominated by the next-to-leading power contributions for a very wide p T range. The large next-to-leading order corrections of NRQCD are absorbed into the leading order of the first power correction. The impact of this finding on heavy quarkonium production and its polarization is discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Towards a Resolution of the Proton Form Factor Problem: New Electron and Positron Scattering Data

There is a significant discrepancy between the values of the proton electric form factor, GpE, extracted using unpolarized and polarized electron scattering. Calculations predict that small two-photon exchange (TPE) contributions can significantly affect the extraction of GpE from the unpolarized electron-proton cross sections. We determined the TPE contribution by measuring the ratio of positron-proton to electron-proton elastic scattering cross sections using a simultaneous, tertiary electron-positron beam incident on a liquid hydrogen target and detecting the scattered particles in the Jefferson Lab CLAS detector. This novel technique allowed us to cover a wide range in virtual photon polarization (epsilon) and momentum transfer (Q2) simultaneously, as well as to cancel luminosity-related systematic errors. The cross section ratio increases with decreasing ε at Q2=1.45 GeV2. This measurement is consistent with the size of the form factor discrepancy at Q2≈1.75 GeV2 and with hadronic calculations including nucleon and Delta intermediate states, which have been shown to resolve the discrepancy up to 2-3 GeV2.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

Dissecting Soft Radiation with Factorization

An essential part of high-energy hadronic collisions is the soft hadronic activity that underlies the primary hard interaction. It includes soft radiation from the primary hard partons, secondary multiple parton interactions (MPI), and factorization-violating effects. The invariant mass spectrum of the leading jet in $Z+\mathrm{jet}$ and $H+\mathrm{jet}$ events is directly sensitive to these effects, and we use here a QCD factorization theorem to predict its dependence on the jet radius $R$, jet ${p}_{T}$, jet rapidity, and partonic process for both the perturbative and nonperturbative components of primary soft radiation. We prove that the nonperturbative contributions involve only odd powers of $R$, and the linear $R$ term is universal for quark and gluon jets. The hadronization model in Pythia8 agrees well with these properties. The perturbative soft initial state radiation (ISR) has a contribution that depends on the jet area in the same way as the underlying event, but this degeneracy is broken by dependence on the jet ${p}_{T}$. The size of this soft ISR contribution is proportional to the color state of the initial partons, yielding the same positive contribution for $gg{\rightarrow}Hg$ and $gq{\rightarrow}Zq$, but a negative interference contribution for $q\overline{q}{\rightarrow}Zg$. Hence, measuring these dependencies allows one to separate hadronization, soft ISR, and MPI contributions in the data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Embedding via the Exact Factorization Approach

We present a quantum electronic embedding method derived from the exact factorization approach to calculate static properties of a many-electron system. The method is exact in principle but the practical power lies in utilizing input from a low-level calculation on the entire system in a high-level method computed on a small fragment, as in other embedding methods. Here, the exact factorization approach defines an embedding Hamiltonian on the fragment. Further, various Hubbard models demonstrate that remarkably accurate ground-state energies are obtained over the full range of weak to strongly correlated systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Ab Initio Structure Factors for Spin-Dependent Dark Matter Direct Detection

We present converged ab initio calculations of structure factors for elastic spin-dependent WIMP scattering off all nuclei used in dark matter direct-detection searches: 19 F, 23 Na, 27 Al, 29 Si, 73 Ge, 12 7I, and 129,131 Xe. From a set of established two- and three-nucleon interactions derived within chiral effective field theory, we construct consistent WIMP-nucleon currents at the one-body level, including effects from axial-vector two-body currents. We then apply the in-medium similarity renormalization group to construct effective valence-space Hamiltonians and consistently transformed operators of nuclear responses. Combining the recent advances of natural orbitals with three-nucleon forces expressed in large spaces, we obtain basis-space converged structure factors even in heavy nuclei. Generally results are consistent with previous calculations but large uncertainties in 127 I highlight the need for further study.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Precision Determination of the Neutral Weak Form Factor of Ca 48

In this work, we report a precise measurement of the parity-violating asymmetry $A_{\rm PV}$ in the elastic scattering of longitudinally polarized electrons from $^{48}{\rm Ca}$. We measure $A_{\rm PV} =2668\pm 106\ {\rm (stat)}\pm 40\ {\rm (syst)}$ parts per billion, leading to an extraction of the neutral weak form factor $F_{\rm W} (q=0.8733$ fm$^{-1}) = 0.1304 \pm 0.0052 \ {\rm (stat)}\pm 0.0020\ {\rm (syst)}$ and the charge minus the weak form factor $F_{\rm ch} - F_{\rm W} = 0.0277\pm 0.0055$. The resulting neutron skin thickness $R_n-R_p=0.121 \pm 0.026\ {\rm (exp)} \pm 0.024\ {\rm (model)}$~fm is relatively thin yet consistent with many model calculations. The combined CREX and PREX results will have implications for future energy density functional calculations and on the density dependence of the symmetry energy of nuclear matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Even-Denominator Fractional Quantum Hall State at Filling Factor ν = 3 / 4

Fractional quantum Hall states (FQHSs) exemplify exotic phases of low-disorder two-dimensional (2D) electron systems when electron-electron interaction dominates over the thermal and kinetic energies. Particularly intriguing among the FQHSs are those observed at even-denominator Landau level filling factors, as their quasiparticles are generally believed to obey non-Abelian statistics and be of potential use in topological quantum computing. Such states, however, are very rare and fragile, and are typically observed in the excited Landau level of 2D electron systems with the lowest amount of disorder. Here we report the observation of a new and unexpected even-denominator FQHS at filling factor ν = 3/4 in a GaAs 2D hole system with an exceptionally high quality (mobility). Furthermore, our magnetotransport measurements reveal a strong minimum in the longitudinal resistance at ν = 3/4, accompanied by a developing Hall plateau centered at (h/e 2 )/(3/4). This even-denominator FQHS is very unusual as it is observed in the lowest Landau level and in a 2D hole system. While its origin is unclear, it is likely a non-Abelian state, emerging from the residual interaction between composite fermions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Quantum Monte Carlo Calculations of Magnetic Form Factors in Light Nuclei

Here, we present Quantum Monte Carlo calculations of magnetic form factors in A = 6-10 nuclei, based on Norfolk two- and three-nucleon interactions, and associated one- and two-body electromagnetic currents. Agreement with the available experimental data for 6 Li, 7 Li, 9 Be and 10 B up to values of momentum transfer q ~ 3 fm -1 is achieved when two-nucleon currents are accounted for. We present a set of predictions for the magnetic form factors of 7 Be, 8 Li, 9 Li, and 9 C. In these systems, two body currents account for ~ 40-60% of the total magnetic strength. Measurements in any of these radioactive systems would provide valuable insights on the nuclear magnetic structure emerging from the underlying many-nucleon dynamics. A particularly interesting case is that of 7 Be, as it would enable investigations of the magnetic structure of mirror nuclei

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms

The crystal structures of the eubacterial translation initiation factor 2 in apo form and with bound GDP and GTP reveal conformational changes upon nucleotide binding and hydrolysis, notably of the catalytically important histidine in the switch II region. Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2 is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2–GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

Ensemble-refinement analysis of native and mutant factor D (FD) crystal structures indicates a dynamical transition in FD from a self-inhibited inactive conformation to a substrate-bound active conformation that is reminiscent of the allostery in thrombin. Comparison with previously observed dynamics in thrombin using NMR data supports the crystallographic ensembles. Human factor D (FD) is a self-inhibited thrombin-like serine proteinase that is critical for amplification of the complement immune response. FD is activated by its substrate through interactions outside the active site. The substrate-binding, or ‘exosite’, region displays a well defined and rigid conformation in FD. In contrast, remarkable flexibility is observed in thrombin and related proteinases, in which Na{sup +} and ligand binding is implied in allosteric regulation of enzymatic activity through protein dynamics. Here, ensemble refinement (ER) of FD and thrombin crystal structures is used to evaluate structure and dynamics simultaneously. A comparison with previously published NMR data for thrombin supports the ER analysis. The R202A FD variant has enhanced activity towards artificial peptides and simultaneously displays active and inactive conformations of the active site. ER revealed pronounced disorder in the exosite loops for this FD variant, reminiscent of thrombin in the absence of the stabilizing Na{sup +} ion. These data indicate that FD exhibits conformational dynamics like thrombin, but unlike in thrombin a mechanism has evolved in FD that locks the unbound native state into an ordered inactive conformation via the self-inhibitory loop. Thus, ensemble refinement of X-ray crystal structures may represent an approach alternative to spectroscopy to explore protein dynamics in atomic detail.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

pyDiSCaMB : enabling the use of multipolar scattering factors in Phenix

Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces pyDiSCaMB , a Python software package designed to integrate between the computational crystallography toolbox ( cctbx ) and the quantum crystallography library DiSCaMB ( Densities in Structural Chemistry and Molecular Biology ), thus enabling multipolar scattering models in Phenix 's toolkit. The implementation, features and capabilities of pyDiSCaMB are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The pyDiSCaMB library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).

MATTS data bank↗
DOE OSTI2015

Cloning, expression, purification and crystallization of a pair of novel virulence factors, SghA and SghR, from Agrobacterium tumefaciens

The crystallization of the novel virulence factors SghA and SghR is reported. Two proteins, SghA and SghR, which were recently identified and characterized as novel bacterial virulence factors regulating the infection of plant hosts by Agrobacterium, were cloned, overexpressed and purified with high yield. Both SghA and SghR form dimers in solution. The purified SghA and SghR were crystallized and the crystals diffracted to 1.9 and 2.1 Å resolution, respectively. Data were collected and processed, and the crystallographic parameters were within acceptable ranges. These results will help in the determination of their structures in order to uncover the molecular mechanism of how these two proteins together control the release of plant defence signals against agrobacteria during pathogen–host interaction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Crystal structure of N-terminally hexahistidine-tagged Onchocerca volvulus macrophage migration inhibitory factor-1

Onchocerca volvulus causes blindness, onchocerciasis, skin infections and devastating neurological diseases such as nodding syndrome. New treatments are needed because the currently used drug, ivermectin, is contraindicated in pregnant women and those co-infected with Loa loa . The Seattle Structural Genomics Center for Infectious Disease (SSGCID) produced, crystallized and determined the apo structure of N-terminally hexahistidine-tagged O. volvulus macrophage migration inhibitory factor-1 (His- Ov MIF-1). Ov MIF-1 is a possible drug target. His- Ov MIF-1 has a unique jellyfish-like structure with a prototypical macrophage migration inhibitory factor (MIF) trimer as the `head' and a unique C-terminal `tail'. Deleting the N-terminal tag reveals an Ov MIF-1 structure with a larger cavity than that observed in human MIF that can be targeted for drug repurposing and discovery. Removal of the tag will be necessary to determine the actual biological oligomer of Ov MIF-1 because size-exclusion chomatographic analysis of His- Ov MIF-1 suggests a monomer, while PISA analysis suggests a hexamer stabilized by the unique C-terminal tails.

Kimble, Amber D. (ORCID:0000000167851596)↗
DOE OSTI2016

UHM–ULM interactions in the RBM39–U2AF65 splicing-factor complex

RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein–protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39–U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35–U2AF65 and RBM39–SF3b155, the RBM39-UHM–U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM–ULM binding interface, providing a rationale for the known specificity of UHM–ULM interactions. This study therefore establishes a structural basis for specific UHM–ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.

Stepanyuk, Galina A.↗