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At least 1,387 records · Page 77

BioTransformer 3.0 – A Web Server for Accurately Predicting Metabolic Transformation Products

BioTransformer 3.0 is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. It combines machine learning approaches with a rule-based system to predict small-molecule metabolism in human tissues, the human gut as well as the external environment (soil and water microbiota). Simply stated, BioTransformer takes a molecular structure as input (SMILES or SDF) and outputs an interactively viewable/sortable table of the predicted metabolites or transformation products (SMILES, PNG images) along with the enzymes that are predicted to be responsible for those reactions and richly annotated downloadable files (CSV and JSON). The entire process typically takes a few seconds. Previous versions of BioTransformer focused exclusively on predicting the metabolism of xenobiotics (such as plant natural products, drugs, cosmetics and other synthetic compounds) using a limited number of pre-defined steps and somewhat limited rule-based methods. BioTransformer 3.0, uses much more sophisticated methods and incorporates new databases, new constraints and new prediction modules to not only more accurately predict the metabolic transformation products of exogenous xenobiotics but also the transformation products of endogenous metabolites, such as amino acids, peptides, carbohydrates, organic acids, and lipids. BioTransformer 3.0 can also support customized sequential combinations of these transformations along with multiple iterations to simulate multi-step human and/or environmental biotransformation events. Performance tests indicate that BioTransformer 3.0 is 40-50% more accurate, much less prone to combinatorial “explosions” and far more comprehensive in terms of metabolite coverage/capabilities than previous versions of BioTransformer.

59 BASIC BIOLOGICAL SCIENCES↗

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.

Fiamenghi, Mateus B↗

Development of a Data Overflow Protection System for Super-Kamiokande to Maximize Data from Nearby Supernovae

Neutrinos from very nearby supernovae, such as Betelgeuse, are expected to generate more than ten million events over 10 s in Super-Kamokande (SK). At such large event rates, the buffers of the SK analog-to-digital conversion board (QBEE) will overflow, causing random loss of data that are critical for understanding the dynamics of the supernova explosion mechanism. In order to solve this problem, two new data-acquisition (DAQ) modules were developed to aid in the observation of very nearby supernovae. The first of these, the SN module, is designed to save only the number of hit photomultiplier tubes during a supernova burst and the second, the Veto module, prescales the high-rate neutrino events to prevent the QBEE from overflowing based on information from the SN module. In the event of a very nearby supernova, these modules allow SK to reconstruct the time evolution of the neutrino event rate from beginning to end using both QBEE and SN module data. This paper presents the development and testing of these modules together with an analysis of supernova-like data generated with a flashing laser diode. We demonstrate that the Veto module successfully prevents DAQ overflows for Betelgeuse-like supernovae as well as the long-term stability of the new modules. During normal running the Veto module is found to issue DAQ vetos a few times per month resulting in a total dead-time less than 1 ms, and does not influence ordinary operations. Additionally, using simulation data we find that supernovae closer than 800 pc will trigger the Veto module, resulting in a prescaling of the observed neutrino data.

F20 Instrumentation and technique↗

Dose Coefficients for Internal Dose Assessments for Exposure to Radioactive Fallout

This paper presents values as well as the bases for calculating internal dose coefficients suitable for estimating organ doses from the exposure to radioactive fallout that could result from the detonation of a nuclear fission device. The 34 radionuclides discussed are the same as those given in a priority list of radionuclides for fallout dose assessments presented in a companion overview paper. The radionuclides discussed are those that are believed to account for a preponderance of the organ doses that might be received by intake by persons of all ages (including in utero and via breast feeding for infants) following exposure to radioactive fallout. The presented dose coefficients for ingestion account for age and include modifications for variations in solubility with distance as discussed previously in the literature, and those for inhalation similarly account for age, solubility, and particle sizes that would be relevant at various distances of exposure as discussed in a companion paper on ingestion dose methods. The proposed modifications peculiar to radioactive fallout account for systematic changes in solubility and particle sizes with distance from the site of detonation, termed here as the region of “local fallout” and the region “beyond local fallout.” Brief definitions of these regions are provided here with more detailed discussion in a companion paper on estimating deposition of fallout radionuclides. This paper provides the dose coefficients for ingestion and inhalation (for particle sizes of 1 μm, 5 μm, 10 μm, and 20 μm) for the region “local fallout.” These dose coefficients for “local fallout” are specific for particles formed in a nuclear explosion that can be large and have radionuclides, particularly the more refractory ones, distributed throughout the volume where the radionuclide has reduced solubility. The dose coefficients for the region “beyond local fallout” are assumed to be the ones published by the International Commission on Radiological Protection (ICRP) in 1995. Comparisons of the presented dose coefficients are made with values published by the ICRP.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Synthetic diversity in the preparation of metallic uranium

Uranium metal is associated with several aspects of nuclear technology; it is used as fuel for research and power reactors, targets for medical isotope productions, explosive for nuclear weapons and precursors in synthetic chemistry. The study of uranium metal at the laboratory scale presents the opportunity to evaluate metallic nuclear fuels, develop new methods for metallic spent fuel reprocessing and advance the science relevant to nuclear forensics and medical isotope production. Since its first isolation in 1841, from the reaction of uranium chloride and potassium metal, uranium metal has been prepared by solid-state reactions and in solution by electrochemical, chemical and radiochemical methods. The present review summarizes the methods outlined above and describes the chemistry associated with each preparation.

36 MATERIALS SCIENCE↗

Bayesian analysis of the 86 Sr ⁢(𝛼,𝛼) reaction to constrain the 86 Sr ⁢(𝛼,𝑛) cross section at astrophysical energies

The alpha optical model potential (𝛼-OMP ) is a phenomenological approach used to describe elastic scattering where multiple reaction channels are open. It is one of the most critical inputs for the calculation of thermonuclear reaction rates in explosive stellar environments, but uncertainties within the 𝛼-OMP lead to imprecise predictions hindering comparisons between calculations and observations. In order to improve the precision of the 𝛼-OMP, additional nuclear physics data are required. In this paper, a measurement of the 86 Sr (𝛼, 𝛼) elastic scattering cross section at multiple energies is reported. Here, a local optical potential is constructed via a fully Bayesian analysis of the elastic scattering data. The resulting uncertainties on the low-energy cross sections relevant to nuclear astrophysics are then calculated and shown to be on the order of 50%.

59 ≤ A ≤ 89↗

Simultaneous imaging of vibrational, rotational, and electronic wave-packet dynamics in a triatomic molecule

Light-induced molecular dynamics often involve the excitation of several electronic, vibrational, and rotational states. Since the ensuing electronic and nuclear motion determines the pathways and outcomes of photoinduced reactions, our ability to monitor and understand these dynamics is crucial for molecular physics, physical chemistry, and photobiology. However, characterizing this complex motion represents a significant challenge when different degrees of freedom are strongly coupled. In this Letter, we demonstrate how the interplay between vibrational, rotational, and electronic degrees of freedom governs the evolution of molecular wave packets in the low-lying states of strong-field-ionized sulfur dioxide. Using time-resolved Coulomb explosion imaging (CEI) and quantum mechanical wave packet simulations, we directly map the bending vibrations of the molecule, show how the vibrational wave packet is influenced by molecular alignment, and elucidate the consequences of nuclear motion for the coupling between the two lowest electronic states of the cation. Furthermore, our results demonstrate that multicoincident CEI can be an efficient experimental tool for characterizing coupled electronic and nuclear motion in polyatomic molecules.

Atomic & molecular processes in external fields↗

Low-energy 17 O(𝑛,𝛾)⁢ 18 O reaction within the microscopic potential model and its role for the weak 𝑟 process

The neutron radiative capture reaction 17 O ⁡(𝑛,𝛾) ⁢18 O plays a pivotal role in both nuclear structure studies and astrophysical nucleosynthesis, particularly in the formation of elements during hydrostatic and explosive stellar environments. We calculated the 17 O ⁡(𝑛,𝛾) ⁢18 O cross section within the Skyrme Hartree-Fock potential model and analyzed electric dipole 𝐸⁢1 transitions to both positive- and negative-parity states below the α-decay threshold in 18 O. Our cross sections are significantly different from the data available in commonly used libraries. We further investigate the impact of the new calculated cross section on weak 𝑟-process nucleosynthesis using large-scale reaction network calculations across a wide range of electron fractions and entropies. Our results show that the 17 O ⁡(𝑛,𝛾) ⁢18 O reaction rate significantly influences the production of first 𝑟-process peak elements, such as strontium, under specific astrophysical conditions. This study highlights the importance of accurate nuclear data for light isotopes in modeling heavy-element synthesis and provides updated reaction rates for future nucleosynthesis simulations.

6 ≤ A ≤ 19↗

First identification of resonant states in the {sup 45}V(p, {gamma}){sup 46}Cr reaction and their influence on the production of {sup 44}Ti in Core Collapse Supernovae

The observation of active 44Ti in supernova remnants offers the potential to solve one of the most debated questions in modern astrophysics, the exact underlying explosion mechanism of core collapse supernovae (CCSNe). In particular, a comparison between the predicted synthesized yield of 44Ti and the ejected flux is expected to allow for a determination of the mass cut of the star. Unfortunately, such comparisons are currently severely hindered by large uncertainties in the nuclear reactions governing the production and destruction of 44Ti. On this note, the astrophysical 45Vðp; γÞ46Cr reaction is expected to play a decisive role. We present the first experimental information on resonant states in the 45Vðp; γÞ46Cr reaction. Excitation energies have been measured with high precision for ten previously unknown, low-spin, proton-unbound states in 46Cr, and spin-parity-assignment constraints have been made using observed γ-decay patterns and shell-model calculations. We find that an l ¼ 1 resonance at 714 keV dominates the 45Vðp; γÞ46Cr reaction for the entire temperature range of α-rich freezeout. Moreover, the nominal rate is found to be ∼25–50% of previous estimates for T > 1.2 GK, indicating an increase in 44Ti production in CCSNe of ∼20–35%.

Cousins, C↗

Strong-field ionization of water: Nuclear dynamics revealed by varying the pulse duration

Polyatomic molecules in strong laser fields can undergo substantial nuclear motion within tens of femtoseconds. Ion imaging methods based on dissociation or Coulomb explosion therefore have difficulty faithfully recording the geometry dependence of the field ionization that initiates the dissociation process. Here we compare the strong-field double ionization and subsequent dissociation of water (both H 2 O and D 2 O) in 10-fs and 40-fs 800-nm laser pulses. We find that 10-fs pulses turn off before substantial internuclear motion occurs, whereas rapid internuclear motion can take place during the double ionization process for 40-fs pulses. The short-pulse measurements are consistent with a simple tunnel ionization picture whose predictions help interpret the motion observed in the long-pulse measurements.

74 ATOMIC AND MOLECULAR PHYSICS↗

Fate of multiparticle resonances: From Q-balls to 3 He droplets

We study a system of N nonrelativistic particles which form a near-threshold resonance. Assuming no subset of these particles can form a bound state, the resonance can only decay through an “explosion” into N particles. We find that the decay width of the resonance scales as E Δ –5/2 in the limit when the energy E of the resonance goes to zero, where Δ is the ground-state energy of a system of N particles in a spherical harmonic trap with unit frequency. Here, the formula remains valid when some pairs of final particles have zero-energy s-wave resonance, but the Efimov effect is not present. In the limit of large N, we show that the final particles follow a Maxwell-Boltzmann distribution if they are bosons and a semicirclelike law if they are fermions. We expect our general result to be applicable to various systems that exist in nature. In particular, we argue that metastable 3 He droplets exist with the lifetime varying over many orders of magnitude ranging from a fraction of a nanosecond to values greatly exceeding the age of the Universe.

74 ATOMIC AND MOLECULAR PHYSICS↗

Primary $\gamma$-ray intensities and $\gamma$-strength functions from discrete two-step $\gamma$-ray cascades in radiative proton-capture experiments

Background: Reaction rates of radiative capture reactions can play a crucial role in the nucleosynthesis of heavy nuclei in explosive stellar environments. These reaction rates depend strongly on $\gamma$-ray decay widths in the reaction products, which are, for nonresonant capture reactions at high excitation energies, derived from the $\gamma$-ray strength function and the nuclear level density. Recently, the ratio method was applied to primary $\gamma$ rays observed from ($\textit{d, p}$) reactions and nuclear resonance fluorescence measurements to extract the dipole strength in atomic nuclei and to test the generalized Brink-Axel hypothesis. Purpose: The purpose of this work is to apply the ratio method to primary $\gamma$-ray intensities of the 63,65 Cu($\textit{p},\gamma$) reactions to extract $\gamma$-ray strength information on the nuclei 64,66 Zn. Here, the impact of spin distribution, total $\gamma$-ray decay widths, level densities, and width fluctuations on the application of the ratio method will be discussed. Additionally, by comparing the relative $\gamma$-ray strength at different excitation energies, conclusions on the validity of the generalized Brink-Axel hypothesis can be made. Method: The radiative proton capture reaction measurements have been performed at the HORUS $\gamma$-ray spectrometer of the University of Cologne at one excitation energy for each reaction. Primary $\gamma$-ray intensities have been determined by normalizing secondary $\gamma$-ray transitions in two-step cascades using their absolute branching ratio. The ratio method was applied to the measured primary $\gamma$-ray intensities as well as to previous measurements by Erlandsson et al. at different excitation energies. Results: The relative strength function curve for 64 Zn from our measurement shows no significant deviation from the previous measurement at a different excitation energy. The same is true for 66 Zn where both measurements were at almost the same excitation energy. Absolute $\gamma$-strength function values have been obtained by normalizing the relative curves to quasiparticle random phase approximation calculations because of the absence of experimental data in the respective energy region. Conclusion: The generalized Brink-Axel hypothesis, i.e., the independence of the strength function on the excitation energy, seems to hold in the studied energy region and nuclei. The method to obtain primary $\gamma$-ray intensities from two-step cascade spectra was shown to be a valuable and sensitive tool although its uncertainties are connected to the knowledge of the low-energy level scheme of the investigated nucleus. The scaling in the ratio method should be taken with care, because the relative strength is not a simple sum of $f_{E1}$ and $f_{M1}$ but a somewhat complex linear combination dependent on the excitation energy of the nucleus.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Persistence of the Z = 28 shell gap in A = 75 isobars: Identification of a possible ( 1 / 2 – ) μ s isomer in Co 75 and β decay to Ni 75

Here, the evolution of shell structure around doubly magic exotic nuclei is of great interest in nuclear physics and astrophysics. In the ‘southwest’ region of 78 Ni, the development of deformation might trigger a major shift in our understanding of explosive nucleosynthesis. To this end, new spectroscopic information on key close-lying nuclei is very valuable. We intend to measure the isomeric and β decay of 75 Co, with one-proton and two-neutron holes relative to 78Ni, to access new nuclear structure information in 75 Co and its β-decay daughters 75 Ni and 74 Ni. The nucleus 75 Co is produced in relativistic in-flight fission reactions of 238 U at the Radioactive Ion Beam Factory in the RIKEN Nishina Center. Its isomeric and β decay are studied exploiting the BigRIPS and EURICA setups. We obtain partial β-decay spectra for 75 Ni and 74 Ni, and report a new isomeric transition in 75 Co. The energy [E γ = 1914(2)keV] and half-life [t 1/2 = 13(6) μs] of the delayed γ ray lend support for the existence of a J π = (1/2 – ) isomeric state at 1914(2) keV. A comparison with PFSDG-U shell-model calculations provides a good account for the observed states in 75 Ni, but the first calculated 1/2 – level in 75 Co, a prolate K = 1/2 state, is predicted about 1 MeV below the observed (1/2 – ) level. The spherical-like structure of the lowest-lying excited states in 75 Ni is proved. In the case of 75 Co, the results suggest that the dominance of the spherical configurations over the deformed ones might be stronger than expected below 78 Ni. Further experimental efforts to discern the nature of the J π = (1/2 – ) isomer are necessary.

59 ≤ A ≤ 89↗

Mass measurements of neutron-rich nuclei near $N = 70$

The astrophysical origin for the chemical elements between the first and second r-process peaks is a matter of intense debate, with a number of nucleosynthesis processes at explosive stellar environments possibly contributing to their production. Reliable data on the trends of neutron separation energies of neutron-rich isotopes are required to model neutron-capture processes that would produce these elements. Masses of 104 Y, 106 Zr, 112 Mo, and 115 Tc have been measured with the time-of-flight-magnetic-rigidity (ToF–Bρ) technique at the National Superconducting Cyclotron Laboratory at Michigan State University. The experiment is the first application of the ToF–Bρ technique at the S800 spectrograph that reached the mass region relevant to heavy-element nucleosynthesis. Finally, the two-neutron separation energy deduced from the measured masses exhibits a smooth trend consistent with the theoretical predictions within the range of experimental uncertainty, indicating that there is no sudden shape transition in these isotopes as hinted at by previous data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Electrical conductivity of a warm neutron star crust in magnetic fields: Neutron-drip regime

We compute the anisotropic electrical conductivity tensor of the inner crust of a compact star at nonzero temperature by extending a previous work on the conductivity of the outer crust. The physical scenarios, where such crust is formed, involve protoneutron stars born in supernova explosions, binary neutron star mergers, and accreting neutron stars. The temperature-density range studied covers the transition from a semidegenerate to a highly degenerate electron gas and assumes that the nuclei form a liquid, i.e., the temperature is above the melting temperature of the lattice of nuclei. The electronic transition probabilities include (i) the screening of electron-ion interaction in the hard-thermal-loop approximation for the QED plasma, (ii) the correlations of the ionic component in a one-component plasma, and (iii) finite nuclear size effects. The conductivity tensor is obtained from the Boltzmann kinetic equation in relaxation time approximation accounting for the anisotropy introduced by a magnetic field. The sensitivity of the results towards the matter composition of the inner crust is explored by using several compositions of the inner crust, which were obtained using different nuclear interactions and methods of solving the many-body problem. The standard deviations of relaxation time and components of the conductivity tensor from the average are below ≤25% except close to crust-core transition, where nonspherical nuclear structures are expected. Finally, our results can be used in dissipative magnetohydrodynamics simulations of warm compact stars.

Physics↗

Time scales for nonlinear processes in preheating after multifield inflation with nonminimal couplings

We have conducted extensive lattice simulations to study the postinflation dynamics of multifield models involving nonminimal couplings. In this work, we explore the parameter dependence of preheating in these models and describe the various time scales that control such nonlinear processes as energy transfer, rescattering, and the approach to radiation domination and thermalization. In the limit of large nonminimal couplings ($ξ_I$ ~ 100), we find that efficient transfer of energy from the inflaton condensate to radiative degrees of freedom, emergence of a radiation-dominated equation of state, and the onset of thermalization each consistently occur within $N_{\text{reh}} ≲ 3 e$-folds after the end of inflation, largely independent of the values of the other couplings in the models. The exception is the case of negative ellipticity, in which there is a misalignment between the dominant direction in field space along which the system evolves and the larger of the nonminimal couplings $ξ_I$. In those cases, the field-space-driven parametric resonance is effectively shut off. More generally, the competition between the scalar fields’ potential and the field-space manifold structure can yield interesting phenomena such as two-stage resonances. Across many regions of parameter space, we find efficient re-scattering between the distinct fields, leading to a partial memory loss of the shape of the initial fluctuation spectrum. Despite the explosive particle production, which can lead to a quick depletion of the background energy density, the nonlinear processes do not induce any superhorizon correlations after the end of inflation in these models, which keeps predictions for cosmic microwave background observables unaffected by the late-time amplification of isocurvature fluctuations. Hence the excellent agreement between primordial observables and recent observations is preserved for this class of models, even when we consider postinflation dynamics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Dark Higgs dark matter

A new U(1) dark gauge group coupled to the Standard Model (SM) via the kinetic mixing portal provides a natural dark matter candidate in the form of the Higgs field, hd, responsible for generating the mass of the dark photon, γ d . We show that the condition m h d ≤m γ d , together with smallness of the kinetic mixing parameter, ϵ, and/or dark gauge coupling, g d , leads the dark Higgs to be sufficiently metastable to constitute dark matter. We analyze the Universe's thermal history and show that both freeze-in, SM→{γ d ,h d }, and freeze-out, {γ d ,h d }→SM, processes can lead to viable dark Higgs dark matter with a sub-GeV mass and a kinetic mixing parameter in the range 10 –13 ≲ϵ≲10 –6 . Observable signals in astrophysics and cosmology include modifications to primordial elemental abundances, altered energetics of supernovae explosions, dark Higgs decays in the late Universe, and dark matter self-interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗