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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

CFM-ID 4.0 – a web server for accurate MS-based metabolite identification

The CFM-ID 4.0 web server (https://cfmid.wishartlab.com) is an online tool for predicting, annotating and interpreting tandem mass (MS/MS) spectra of small molecules. It is specifically designed to assist researchers pursuing studies in metabolomics, exposomics and analytical chemistry. More specifically, CFM-ID 4.0 supports the: 1) prediction of electrospray ionization quadrupole time-of-flight tandem mass spectra (ESI-QTOF-MS/MS) for small molecules over multiple collision energies (10 eV, 20 eV, and 40 eV); 2) annotation of ESI-QTOF-MS/MS spectra given the structure of the compound; and 3) identification of a small molecule that generated a given ESI-QTOF-MS/MS spectrum at one or more collision energies. The CFM-ID 4.0 web server makes use of a substantially improved MS fragmentation algorithm, a much larger database of experimental and in silico predicted MS/MS spectra and improved scoring methods to offer more accurate MS/MS spectral prediction and MS/MS-based compound identification. Compared to earlier versions of CFM-ID, this new version has an MS/MS spectral prediction performance that is ~22% better and a compound identification accuracy that is ~35% better on a standard (CASMI 2016) testing dataset. CFM-ID 4.0 also features a neutral loss function that allows users to identify similar or substituent compounds where no match can be found using CFM-ID’s regular MS/MS-to-compound identification utility. Finally, the CFM-ID 4.0 web server now offers a much more refined user interface that is easier to use, supports molecular formula identification (from MS/MS data), provides more interactively viewable data (including proposed fragment ion structures) and displays MS mirror plots for comparing predicted with observed MS/MS spectra. These improvements should make CFM-ID 4.0 much more useful to the community and should make small molecule identification much easier, faster, and more accurate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å

HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG↓C-3' in duplex DNA and cleaves (‘↓’) to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 Å. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded β sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the ‘PD-D/EXK’ superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G↓CGC) and MspI (C↓CGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nuclear structure opportunities with GeV radioactive beams at FAIR

The Facility for Antiproton and Ion Research (FAIR) is in its final construction stage next to the campus of the Gesellschaft für Schwerionenforschung Helmholtzzentrum for heavy-ion research in Darmstadt, Germany. Once it starts its operation, it will be the main nuclear physics research facility in many basic sciences and their applications in Europe for the coming decades. Owing to the ability of the new fragment separator, Super-FRagment Separator, to produce high-intensity radioactive ion beams in the energy range up to about 2 GeV/nucleon, these can be used in various nuclear reactions. This opens a unique opportunity for various nuclear structure studies across a range of fields and scales: from low-energy physics via the investigation of multi-neutron systems and halos to high-density nuclear matter and the equation of state, following heavy-ion collisions, fission and study of short-range correlations in nuclei and hypernuclei. Here, the newly developed reactions with relativistic radioactive beams (R3B) set up at FAIR would be the most suitable and versatile for such studies. An overview of highlighted physics cases foreseen at R3B is given, along with possible future opportunities, at FAIR.

FAIR↗
DOE OSTI2025

Time-Dependent Density Functional Theory Description of 238 U⁡(n,f), 240,242 Pu⁢(n,f), and 237 Np(n,f) Reactions

In nuclei with an odd nucleon number the nonvanishing spin number density is the source of a pseudomagnetic field, which favors the splitting of the nucleon Cooper pairs. Such a pseudomagnetic field is generated always in the dynamics of any nucleus, but its effects on Cooper pairs are significantly enhanced in the dynamic evolution of nuclei with an odd number of nucleons. We present for the first time a microscopic study of the induced fission of the odd neutron compound nuclei 239 U, 241,243 Pu, and the odd proton, odd neutron compound nucleus 238 Np, performed within the time-dependent density functional theory extended to superfluid fermion systems, without any simplifying assumptions, with controlled numerical approximations, and for a very large number of initial conditions. Because of the presence of the unpaired odd nucleon(s), the time-reversal symmetry of the fission compound nucleus is spontaneously broken, an aspect routinely neglected in the most advanced microscopic approaches of the past. The emerging fission fragment properties are quite similar to the properties of fission fragments of neighboring even-even nuclei. The time from saddle-to-scission is often significantly longer in odd-odd or odd-mass nuclei than for even-even nuclei, since systems with unpaired nucleons are easier to excite and the potential energy surfaces of these nuclei have more structure, often resembling a very complicated obstacle course, rather than a more direct evolution of the nuclear shape from the top of the outer fission barrier to the scission configuration. The Pauli blocking approximation, often invoked in the literature, expected to inhibit the fission of nuclei with unpaired nucleons, is surprisingly strongly violated during the fission dynamics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Muon-induced fission as a probe of the underlying dynamics in nuclear fission

Muon-induced fission could be utilized as a probe to study the underlying dynamics of nuclear fission. Here, the probability of muon attachment to the light asymmetric fission fragment is sensitive to fission dynamics, such as the timescale and friction of the fission event, charge asymmetry, and possibly the shape of the fission fragments. We focus on muonic atoms that are formed with actinide nuclei. A relativistic approach is employed, solving the Dirac equation for the muonic wave function in the presence of a time-dependent electromagnetic field generated by the fissioning nucleus. Computations are carried out on a three-dimensional Cartesian lattice with no symmetry assumptions. The results show a strong dependence of the attachment probability on the fission charge asymmetry and a more modest dependence on friction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Semi-inclusive deep-inelastic scattering on a polarized spin-1 target. I. Cross section and spin observables

We develop the theoretical framework for semi-inclusive deep-inelastic scattering on a polarized spin-1 target and apply it to scattering on the polarized deuteron with spectator nucleon tagging. In Part I (this article) we present the general form of the semi-inclusive cross section and polarization observables for the spin-1 target. A relativistically covariant formulation in terms of four-vectors and invariant polarization parameters is employed. The target polarization is described by a spin density matrix with vector and tensor polarization. The spin and azimuthal angle dependence of the semi-inclusive cross section is derived and parametrized in terms of invariant structure functions. To validate the result, the structure functions are expressed as photon-target helicity amplitudes with known symmetry properties. The expressions presented here are kinematic (no assumptions about particle production dynamics) and valid in all regions of the deep-inelastic final state (current and target fragmentation regions). In Part II (following article), we consider deep-inelastic scattering on the polarized deuteron with spectator nucleon tagging as a special case of target fragmentation. The semi-inclusive structure functions are computed by separating nuclear and hadronic structure, and the polarization observables are explored as functions of the tagged nucleon momentum.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Momentum-resolved above-threshold ionization of deuterated water

We present momentum-resolved coincidence measurements of strong-field single and double ionization of deuterated water (D 2 O) using intense few-cycle laser pulses. We measure the vector momentum of electrons and ions resulting from the laser-molecule interaction. This enables us to measure the photoelectron spectrum for electrons in coincidence with fragment ions having different momenta, which can be related to different final states of the cation and dication. The photoelectron spectra for different fragment ion momenta show striking differences, which can be interpreted in terms of the removal of electrons from different molecular orbitals, including the highest occupied molecular orbital (HOMO), as well as more deeply bound ones (e.g., HOMO-2). Here, we discuss our measurements in light of calculations which model the strong-field light matter interaction.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Dynamics of resonant low-energy electron attachment to ethanol-producing hydroxide anions

Here, the dynamics of dissociative electron attachment to ethanol is experimentally investigated at the Feshbach resonance formed with incident electron energies near 9.5 eV. Highly differential laboratory-frame momentum distributions of OH – fragments are measured for a series of energies spanning the resonance width, using the velocity-map-imaging technique. The OH – kinetic-energy distribution indicates that the C-O breaking dissociation process could either be a three-body dissociation or a two-body dissociation with significant rovibrational excited fragments. The small, but significant, anisotropy in the OH – angular distribution provides signatures of the molecular symmetry of the associated resonant state under the axial recoil approximation, which assumes the dissociation is much faster than any rotation of the dissociation axis. Within these assumptions, the 9.5-eV Feshbach resonance can be assigned to the electronic transition from the ($10a'$) orbital with its ground-state C s symmetry to the empty ($4a''$) level, involving the simultaneous electron attachment. This dynamics could be a model for C-O dissociation in larger alcohols and ethers.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Kinetically constrained freezing transition in a dipole-conserving system

Here, we study a stochastic lattice gas of particles in one dimension with strictly finite-range interactions that respect the fractonlike conservation laws of total charge and dipole moment. As the charge density is varied, the connectivity of the system's charge configurations under the dynamics changes qualitatively. We find two distinct phases: Near half filling the system thermalizes subdiffusively, with almost all configurations belonging to a single dynamically connected sector. As the charge density is tuned away from half filling there is a phase transition to a frozen phase, where locally active finite bubbles cannot exchange particles and the system fails to thermalize. The two phases exemplify what has recently been referred to as weak and strong Hilbert space fragmentation, respectively. We study the static and dynamic scaling properties of this weak-to-strong fragmentation phase transition in a kinetically constrained classical Markov circuit model, obtaining some conjectured exact critical exponents.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

b b ¯ kinematic correlations in cold nuclear matter

Background: The LHCb Collaboration has studied a number of kinematic correlations between B -hadron pairs through their subsequent decays to J / ψ pairs in p + p collisions at 7 and 8 TeV for four minimum values of the J / ψ p T . Purpose: In this work, these measurements are compared to calculations of b b ¯ pairs and their hadronization and inclusive decays to J / ψ J / ψ are compared to the same observables. Potential cold matter effects on the b b ¯ pair observables are discussed to determine which are most likely to provide insights about the system and why. Methods: The calculations, employing the exclusive HVQMNR code, assume the same intrinsic k T -broadening and fragmentation as in prior work. The pair distributions presented by LHCb are calculated in this approach, both for the parent b b ¯ and the J / ψ J / ψ pairs produced in their decays. The sensitivity of the results to the intrinsic k T broadening is shown. The theoretical uncertainties due to the b quark mass and scale variations on both the initial b b ¯ pairs and the resulting J / ψ pairs are also shown, as is the dependence of the results on the rapidity range of the measurement. Possible effects due to the presence of the nucleus are studied by increasing the size of the k T broadening and modifying the fragmentation function. Results: Good agreement with the LHCb data is found for all observables. The parent b b ¯ distributions are more sensitive to the k T broadening than are the final-state J / ψ pairs. Conclusions: Next-to-leading order calculations with k T broadening, as in prior work, can describe all correlated observables. Multiple measurements of correlated observables are sensitive to different nuclear effects which can help distinguish between them.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Invariant-mass spectrum of O 11

The invariant-mass distribution of O 11 fragments formed in two-neutron-knockout reactions with a O 13 projectile and Be 9 target has been also examined. Gating on events where the C 9 decay fragments produced following 2 p emission are recoiled transversely in the projectile's frame improves the overall invariant-mass resolution. The observed peak is now shown to have contributions from at least two O 11 levels, in contradiction with the suggestion of Fortune [ Phys. Rev. C 99 , 051302(R) (2019) ]. The data, yet, do not differentiate between the ground-state properties obtained by the Gamow coupled-channels calculation and the prompt 2 p -decay model of Fortune. The ground-state 2 p -decay energy is 4.25(6) MeV in a two-level fit to the data, but lower values are possible if more states contribute to the observed spectrum, as suggested in the previous analysis.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Low-lying level structure of the neutron-unbound $\textit{N}$ = 7 isotones

This article reports on results of an experimental search for ground state shell inversion in the neutron-unbound $\textit{N}$ = 7 isotones 9 He and 10 Li. Two different radioactive ion beams ( 11 Be, E lab = 44 MeV/u and 12 B, E lab = 45 MeV/u) impinging on a beryllium target were used to directly and selectively populate unbound states of a given ℓ in the nuclides of interest. Be( 11 Be, 8 He + $\textit{n}$) and Be( 12 B, 8 He + $\textit{n}$) reactions populated unbound states in 9 He. Fragments and neutrons were detected in coincidence to reconstruct the decay energy of 9 He using invariant mass spectroscopy. Similarly, Be( 11 Be, 9 Li + $\textit{n}$) and Be( 12 B, 9 Li + $\textit{n}$) reactions were used to populate unbound states in 10 Li, and the time-of-flight method was used to determine the relative velocity of the 9 Li fragments and neutrons in coincidence. Various states in both 9 He and 10 Li were observed and characterized. Here, the data indicate possible ground state shell inversion in both cases.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Neutron-Neutron Correlations in the Photofission of 238U

Background: In the fission of actinides, the nearly back-to-back motion of the fission fragments has a strong effect on the kinematics of fission neutrons. This leads to a favoring of opening angles near 0? and 180? in the neutron-neutron (n-n) opening angle distributions of correlated neutron pairs from the same fission event. Purpose: To measure the n-n opening angle and energy correlations in the photofission of 238U. As of this writing, measurements of correlated n-n opening angle distributions have been reported only for the spontaneous and neutron-induced fission of actinides. This work is the first to report such a measurement using photofission and will provide useful experimental input for photofission models used in codes such as MCNP and FREYA. Method: Fission is induced using bremsstrahlung photons produced via a low duty factor, pulsed, linear electron accelerator. The bremsstrahlung photon beam impinges upon a 238U target that is surrounded by a large neutron scintillation detection system capable of measuring particle position and time of flight, from which n-n opening angle and energy are measured. Neutron-neutron angular correlations are determined by taking the ratio between a correlated neutron distribution and an uncorrelated neutron distribution formed by the pairing of neutrons produced during different beam pulses. This analysis technique greatly diminishes effects due to detector efficiencies, acceptance, and experimental drifts. Results: The angular correlation of neutrons from the photofission of 238U shows a high dependence on neutron energy as well as a dependence on the angle of the emitted neutrons with respect to the incoming photon beam. Angular correlations were also measured using neutrons from the spontaneous fission of 252Cf, showing good agreement with past measurements. Conclusions: The measured angular correlations reflect the underlying back-to-back nature of the fission fragments. An anomalous decline in n-n yield was observed for opening angles near 180? for 238U.

Burggraf, Jeff↗
DOE OSTI2020

Correlation between time and angular alignment in molecular dynamics simulations of heavy ion collisions

Neutron-proton equilibration is a process which has been used to study the density dependence of the symmetry energy term in the nuclear equation-of-state. Here, this study utilizes constrained molecular dynamics (CoMD) simulations of 70 Zn + 70 Zn with collision energies of 35 and 45 MeV/nucleon. An algorithm is used which searches through CoMD events and identifies the PLF* after it separates from the target and determines its lifetime, Δt. It also determines the fragments that the PLF* breaks apart into and determines their angular alignment. This technique gives an opportunity to explore how the average alignment of dynamically produced fragments, $\langle$α $\rangle$ dyn , evolves with PLF* lifetime. An approximately linear relationship was determined with d$\langle$α $\rangle$ dyn /dΔt = 0.98 ± 0.08 rad / zs and 1.06 ± 0.09 rad / zs for the 35 and 45 MeV / nucleon, respectively, indicating a correlation with magnitude consistent with classically determined values which were used for prior experimental studies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Measurement of Charged-Pion Production in Deep-Inelastic Scattering off Nuclei with the CLAS Detector

Background: Energetic quarks in nuclear deep-inelastic scattering propagate through the nuclear medium. Processes that are believed to occur inside nuclei include quark energy loss through medium-stimulated gluon bremsstrahlung and intranuclear interactions of forming hadrons. More data are required to gain a more complete understanding of these effects. Purpose: To test the theoretical models of parton transport and hadron formation, we compared their predictions for the nuclear and kinematic dependence of pion production in nuclei. Methods: We have measured charged-pion production in semi-inclusive deep-inelastic scattering off D, C, Fe, and Pb using the CLAS detector and the CEBAF 5.014-GeV electron beam. We report results on the nuclear-to-deuterium multiplicity ratio for π + and π - as a function of energy transfer, four-momentum transfer, and pion energy fraction or transverse momentum—the first three-dimensional study of its kind. Results: The π + multiplicity ratio is found to depend strongly on the pion fractional energy z and reaches minimum values of 0.67 ± 0.03, 0.43 ± 0.02, and 0.27 ± 0.01 for the C, Fe, and Pb targets, respectively. The z dependencies of the multiplicity ratios for π + and π - are equal within uncertainties for C and Fe targets but show differences at the level of 10% for the Pb-target data. The results are qualitatively described by the GIBUU transport model, as well as with a model based on hadron absorption, but are in tension with calculations based on nuclear fragmentation functions. Conclusions: These precise results will strongly constrain the kinematic and flavor dependence of nuclear effects in hadron production, probing an unexplored kinematic region. They will help to reveal how the nucleus reacts to a fast quark, thereby shedding light on its color structure and transport properties and on the mechanisms of the hadronization process.

Moran, S.↗
DOE OSTI2023

Investigating the time dependence of neutron-proton equilibration using molecular dynamics simulations

Neutron-proton equilibration has previously been studied experimentally in dynamically deformed nuclei in heavy ion collisions [Phys. Rev. Lett. 118, 062501 (2017); Phys. Rev. C 95, 044604 (2017)] using the NIMROD detector array at the Cyclotron Institute at Texas A&M University. Results indicated the composition of the two heaviest fragments originating from the excited projectile-like fragment evolved exponential with respect to their orientation angle to be more similar. Constrained Molecular Dynamics and Antisymmetrized Molecular Dynamics simulations were performed for different formulations of the density dependence of the asymmetry energy term of the nuclear equation of state. The simulations are compared to experimental results, which indicate a better agreement with a softer interaction in the nuclear equation of state.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Description of the multinucleon transfer mechanism for Ca 48 + Pu 244 and Kr 86 + Pt 198 reactions in a quantal transport approach

Multinucleon transfer (MNT) reactions involving heavy projectile and target combinations stand as a promising method for synthesizing new neutron-rich exotic nuclei, which may not be possible using hot or cold fusion reactions or fragmentation. Exploring the mechanisms behind MNT reactions is essential and it requires a comprehensive theoretical framework that can explain the physical observables in these reactions. This work aims to show that the quantal diffusion approach based on the stochastic mean-field (SMF) theory is capable of explaining the reaction dynamics observed in MNT reactions. Primary product mass distributions in 48 Ca + 244 Pu reaction at E c.m. = 203.2 MeV and 86 Kr + 198 Pt reaction at E c.m. = 324.2 MeV are calculated and compared with the available experimental data. In this work, we utilize the time-dependent Hartree-Fock (TDHF) calculations to analyze the mean-field reaction dynamics computationally in the reactions 48 Ca + 244 Pu and 86 Kr + 198 Pt for a broad range of initial angular momenta. Quantal transport description based on the SMF approach is used to calculate quantal diffusion coefficients and mass variances in 48 Ca + 244 Pu and 86 Kr + 198 Pt systems. The primary products arising from quasifission reactions are described by joint probability distribution in the SMF approach and those arising from fusion-fission are estimated by using the statistical deexcitation code gemini + +. Mean values of charge and mass numbers, scattering angles of the primary reaction products, and the total kinetic energies after the collision are calculated within the TDHF framework for a broad range of initial angular momenta. Throughout all the collisions, drift toward the mass symmetry and large mass dispersion associated with this drift are observed. Here, the calculated primary fragment and mass distributions using the SMF approach successfully explain experimental observations for the 48 Ca + 244 Pu and 86 Kr + 198 Pt systems. The primary mass distributions, mean values of binary products, and mass dispersions are determined and results are compared with the available experimental data. The observed agreement between the experimental data and SMF results highlights the effectiveness of the quantal diffusion mechanism based on the SMF approach, which does not include any adjustable parameters other than standard parameters of Skyrme energy density functional.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Relativistic diffusion model for hadron production in p -Pb collisions at energies available at the CERN Large Hadron Collider

We investigate charged-hadron production in relativistic heavy-ion collisions of asymmetric systems within a nonequilibrium-statistical framework. Calculated centrality-dependent pseudorapidity distributions for p-Pb collisions at s NN = 5.02 and 8.16 TeV are compared with data from the Large Hadron Collider. Our approach combines a relativistic diffusion model with formulations based on quantum chromodynamics while utilizing numerical solutions of a Fokker-Planck equation to account for the shift and broadening of the fragmentation sources for particle-production with respect to the stopping (net-baryon) rapidity distributions. To represent the centrality dependence of charged-hadron production in asymmetric systems over a broad region of pseudorapidities, the consideration and precise modeling of the fragmentation sources, along with the central gluon-gluon source, is found to be essential. Specifically, this results in an inversion of the particle-production amplitude from backward to forward dominance when transitioning from central to peripheral collisions, in agreement with recent ATLAS and ALICE p-Pb data at s NN = 5.02 T e V . Published by the American Physical Society 2024

Schulz, Philipp (ORCID:0009000266642148)↗