Machine learning approach to pattern recognition in nuclear dynamics from the ab initio symmetry-adapted no-core shell model

A novel machine learning approach is used to provide further insight into atomic nuclei and to detect orderly patterns amidst a vast data of large-scale calculations. The method utilizes a neural network that is trained on ab initio results from the symmetry-adapted no-core shell model (SA-NCSM) for light nuclei. We show that the SA-NCSM, which expands ab initio applications up to medium-mass nuclei by using dominant symmetries of nuclear dynamics, can reach heavier nuclei when coupled with the machine learning approach. In particular, we find that a neural network trained on probability amplitudes for $s$-and $p$-shell nuclear wave functions not only predicts dominant configurations for heavier nuclei but in addition, when tested for the $^{20}$Ne ground state, it accurately reproduces the probability distribution. The nonnegligible configurations predicted by the network provide an important input to the SA-NCSM for reducing ultra-large model spaces to manageable sizes that can be, in turn, utilized in SA-NCSM calculations to obtain accurate observables. The neural network is capable of describing nuclear deformation and is used to track the shape evolution along the $^{20-42}$Mg isotopic chain, suggesting a shape-coexistence that is more pronounced toward the very neutron-rich isotopes. We provide first descriptions of the structure and deformation of $^{24}$Si and $^{40}$Mg of interest to x-ray burst nucleosynthesis, and even of the extremely heavy nuclei such as $^{166,168}$Er and $^{236}$U, that build upon first principles considerations.Comment: 10 pages, 9 figure

Ab initio translationally invariant nucleon-nucleus optical potentials

We combine the \textit{ab initio} symmetry-adapted no-core shell model (SA-NCSM) with the single-particle Green's function approach to construct optical potentials rooted in first principles. Specifically, we show that total cross sections and phase shifts for neutron elastic scattering from a $^4$He target with projectile energies between 0.5 and 10 MeV closely reproduce the experiment. In addition, we discuss an important new development that resolves a long-standing issue with spurious center-of-mass motion in the Green's function formalism for many-body approaches. The new development opens the path for first-principle predictions of cross sections for elastic scattering of single-nucleon projectiles, nucleon capture and deuteron breakup reactions, feasible for a broad range of open-shell spherical and deformed nuclei in the SA-NCSM approach.Comment: 19 pages, 11 figures, to be submitted to Physical Review

Nucleic Acids Res

The HIV-1 viral infectivity factor (Vif) is required for productive infection of non-permissive cells, including most natural HIV-1 targets, where it counteracts the antiviral activities of the cellular cytosine deaminases APOBEC-3G (A3G) and A3F. Vif is a multimeric protein and the conserved proline-rich domain (161)PPLP(164) regulating Vif oligomerization is crucial for its function and viral infectivity. Here, we expressed and purified wild-type Vif and a mutant protein in which alanines were substituted for the proline residues of the (161)PPLP(164) domain. Using dynamic light scattering, circular dichroism and fluorescence spectroscopy, we established the impact of these mutations on Vif oligomerization, secondary structure content and nucleic acids binding properties. In vitro, wild-type Vif formed oligomers of five to nine proteins, while Vif AALA formed dimers and/or trimers. Up to 40% of the unbound wild-type Vif protein appeared to be unfolded, but binding to the HIV-1 TAR apical loop promoted formation of beta-sheets. Interestingly, alanine substitutions did not significantly affect the secondary structure of Vif, but they diminished its binding affinity and specificity for nucleic acids. Dynamic light scattering showed that Vif oligomerization, and interaction with folding-promoting nucleic acids, favor formation of high molecular mass complexes. These properties could be important for Vif functions involving RNAs

Ab initio single-neutron spectroscopic overlaps in lithium isotopes

We calculate single-neutron spectroscopic overlaps for lithium isotopes in the framework of the \textit{ab initio} symmetry-adapted no-core shell model. We report the associated neutron-nucleus asymptotic normalization coefficients (ANCs) and spectroscopic factors (SFs) that are important ingredients in many reaction cross section calculations. While spectroscopic factors have been traditionally extracted from experimental cross sections, their sensitivity on the type of reactions, energy, and the underlying models point to the need for determining SF from first-principle structure considerations. As illustrative examples, we present $^6$Li+n, $^7$Li+n, and $^8$Li+n, and we show that the results are in a good agreement with those of other \textit{ab initio} methods, where available, including the quantum Monte Carlo approach. We compare ANCs and SFs to available experimentally deduced values, with a view toward expanding this study to heavier nuclei and to extracting inter-cluster effective interactions for input into analyses of existing and future experimental data.Comment: 10 pages, 8 figure

A Drosophila screen identifies NKCC1 as a modifier of NGLY1 deficiency

N-Glycanase 1 (NGLY1) is a cytoplasmic deglycosylating enzyme. Loss-of-function mutations in the NGLY1 gene cause NGLY1 deficiency, which is characterized by developmental delay, seizures, and a lack of sweat and tears. To model the phenotypic variability observed among patients, we crossed a Drosophila model of NGLY1 deficiency onto a panel of genetically diverse strains. The resulting progeny showed a phenotypic spectrum from 0 to 100% lethality. Association analysis on the lethality phenotype, as well as an evolutionary rate covariation analysis, generated lists of modifying genes, providing insight into NGLY1 function and disease. The top association hit was Ncc69 (human NKCC1/2), a conserved ion transporter. Analyses in NGLY1-/- mouse cells demonstrated that NKCC1 has an altered average molecular weight and reduced function. The misregulation of this ion transporter may explain the observed defects in secretory epithelium function in NGLY1 deficiency patients

Optical potentials for the rare-isotope beam era

We review recent progress and motivate the need for further developments in nuclear optical potentials that are widely used in the theoretical analysis of nucleon elastic scattering and reaction cross sections. In regions of the nuclear chart away from stability, which represent a frontier in nuclear science over the coming decade and which will be probed at new rare-isotope beam facilities worldwide, there is a targeted need to quantify and reduce theoretical reaction model uncertainties, especially with respect to nuclear optical potentials. We first describe the primary physics motivations for an improved description of nuclear reactions involving short-lived isotopes, focusing on its benefits for fundamental science discoveries and applications to medicine, energy, and security. We then outline the various methods in use today to build optical potentials starting from phenomenological, microscopic, and ab initio methods, highlighting in particular the strengths and weaknesses of each approach. We then discuss publicly-available tools and resources facilitating the propagation of recent progresses in the field to practitioners. Finally, we provide a set of open challenges and recommendations for the field to advance the fundamental science goals of nuclear reaction studies in the rare-isotope beam era.Comment: This paper is the outcome of the Facility for Rare Isotope Beams Theory Alliance (FRIB - TA) topical program "Optical Potentials in Nuclear Physics" held in March 2022 at FRIB. Its content is non-exhaustive, was chosen by the participants and reflects their efforts related to optical potential

An above-barrier narrow resonance in F-15

Intense and purified radioactive beam of post-accelerated O-14 was used to study the low-lying states in the unbound F-15 nucleus. Exploiting resonant elastic scattering in inverse kinematics with a thick target, the second excited state, a resonance at E-R = 4.757(6)(10) MeV with a width of Gamma = 36(5)(14) keV was measured for the first time with high precision. The structure of this narrow above-barrier state in a nucleus located two neutrons beyond the proton drip line was investigated using the Gamow Shell Model in the coupled channel representation with a C-12 core and three valence protons. It is found that it is an almost pure wave function of two quasi-bound protons in the 2s(1/2) shell. (C) 2016 The Authors. Published by Elsevier B.V

An above-barrier narrow resonance in ¹⁵F

Intense and purified radioactive beam of post-accelerated $^{14}$O was used to study the low-lying states in the unbound $^{15}$F nucleus. Exploiting resonant elastic scattering in inverse kinematics with a thick target, the second excited state, a resonance at E$\_R$=4.757(6)(10)~MeV with a width of $\Gamma$=36(5)(14)~keV was measured for the first time with high precision. The structure of this narrow above-barrier state in a nucleus located two neutrons beyond the proton drip line was investigated using the Gamow Shell Model in the coupled channel representation with a $^{12}$C core and three valence protons. It is found that it is an almost pure wave function of two quasi-bound protons in the $2s\_{1/2}$ shell.Comment: 8 pages, 2 figures, 1 table, Submitted to Phys. Lett.