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At least 1,279 records · Page 71

Host galaxies of ultra-strong Mg ii absorbers at z ∼ 0.7

ABSTRACT We report spectroscopic identification of the host galaxies of 18 ultra-strong Mg ii systems (USMg ii) at 0.6 ≤ z ≤ 0.8. We created the largest sample by merging these with 20 host galaxies from our previous survey within 0.4 ≤ z ≤ 0.6. Using this sample, we confirm that the measured impact parameters ($\rm 6.3\leqslant D[kpc] \leqslant 120$ with a median of 19 kpc) are much larger than expected, and the USMg ii host galaxies do not follow the canonical $\rm {\it W}_{2796}-{\it D}$ anticorrelation. We show that the presence and significance of this anticorrelation may depend on the sample selection. The $\rm {\it W}_{2796}-{\it D}$ anticorrelation seen for the general Mg ii absorbers show a mild evolution at low $\rm W_{2796}$ end over the redshift range 0.4 ≤ z ≤ 1.5 with an increase of the impact parameters. Compared to the host galaxies of normal Mg ii absorbers, USMg ii host galaxies are brighter and more massive for a given impact parameter. While the USMg ii systems preferentially pick star-forming galaxies, they exhibit slightly lower ongoing star-forming rates compared to main sequence galaxies with the same stellar mass, suggesting a transition from star-forming to quiescent states. For a limiting magnitude of mr < 23.6, at least 29 per cent of the USMg ii host galaxies are isolated, and the width of the Mg ii absorption in these cases may originate from gas flows (infall/outflow) in isolated haloes of massive star forming but not starbursting galaxies. We associate more than one galaxy with the absorber in $\ge 21~{{\ \rm per\ cent}}$ cases, where interactions may cause wide velocity spread.

Astronomy & Astrophysics↗

Accurate shear estimation with fourth-order moments

ABSTRACT As imaging surveys progress in exploring the large-scale structure of the Universe through the use of weak gravitational lensing, achieving sub-per cent accuracy in estimating shape distortions caused by lensing, or shear, is imperative for precision cosmology. In this paper, we extend the Fourier power function shapelets (FPFS) shear estimator using fourth-order shapelet moments and combine it with the original second-order shear estimator to reduce galaxy shape noise. We calibrate this novel shear estimator analytically to a sub-per cent level-accuracy using the AnaCal framework. This higher order shear estimator is tested with realistic image simulations, and after analytical correction for the detection/selection bias and noise bias, the multiplicative shear bias $|m|$ is below $3\times 10^{-3}$ (99.7 per cent confidence interval) for both isolated and blended galaxies. Once combined with the second-order FPFS shear estimator, the shape noise is reduced by $\sim 35~{{\ \rm per\ cent}}$ for isolated galaxies in simulations with Hyper Suprime-Cam and Vera C. Rubin Observatory Legacy Survey of Space and Time observational conditions. However, for blended galaxies, the effective number density does not significantly improve with the combination of the two estimators. Based on these results, we recommend exploration of how this framework can further reduce the systematic uncertainties in shear due to point spread function leakage and modelling error, and potentially provide improved precision in shear inference in high-resolution space-based images.

79 ASTRONOMY AND ASTROPHYSICS↗

Cas3-Mediated Genome Reduction: Demonstration in Cupriavidus Necator H16 Improves Growth on Heterotrophic and Autotrophic Carbon Sources

Genome reduction is widely used to improve microbial bioprocessing hosts by reducing the burden of inessential physiology. Rationally identifying genomic regions that are dispensable or even detrimental to bioprocessing is challenged by our inability to map genome sequence to function across complex regulation and physiology. Thus, there is a need for tools that rapidly generate reduced genome strains with improved performance in process-relevant conditions. Here, we report a Cascade-Cas3-enabled method called TRIM3 that generates large deletions by targeting a randomly integrated transposon, enabling facile generation of a genome-reduced mutant library. Mutants with improved performance were isolated following growth-coupled selection and analyzed by long-read DNA sequencing to identify deletions in their genomes. We deploy this system iteratively in the industrial host Cupriavidus necator H16 on fructose and on formate. After two rounds of TRIM3, we isolate a strain containing a total reduction of 1.4 Mb (18.4% of the genome) that grows 25% faster in a bioreactor on fructose and a strain with a total reduction of 0.5 Mb (7.3% of the genome) that grows 14% faster on formate. This work demonstrates a method for random, iterative, growth-selectable genome reduction that represents a new avenue for large-scale genome modifications and the development of improved bioprocessing hosts.

09 BIOMASS FUELS↗

Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid

Abstract We previously described the design of triacetic acid lactone (TAL) biosensor ‘AraC-TAL1’, based on the AraC regulatory protein. Although useful as a tool to screen for enhanced TAL biosynthesis, this variant shows elevated background (leaky) expression, poor sensitivity and relaxed inducer specificity, including responsiveness to orsellinic acid (OA). More sensitive biosensors specific to either TAL or OA can aid in the study and engineering of polyketide synthases that produce these and similar compounds. In this work, we employed a TetA-based dual-selection to isolate new TAL-responsive AraC variants showing reduced background expression and improved TAL sensitivity. To improve TAL specificity, OA was included as a ‘decoy’ ligand during negative selection, resulting in the isolation of a TAL biosensor that is inhibited by OA. Finally, to engineer OA-specific AraC variants, the iterative protein redesign and optimization computational framework was employed, followed by 2 rounds of directed evolution, resulting in a biosensor with 24-fold improved OA/TAL specificity, relative to AraC-TAL1.

Wang, Zhiqing↗

The Melampsora americana Population on Salix purpurea in the Great Lakes Region Is Highly Diverse with a Contributory Influence of Clonality

Shrub willows (Salix spp.) are emerging as a viable lignocellulosic, second-generation bioenergy crop with many growth characteristics favorable for marginal lands in New York State and surrounding areas. Willow rust, caused by members of the genus Melampsora, is the most limiting disease of shrub willow in this region and remains extremely understudied. In this study, genetic diversity, genetic structure, and pathogen clonality were examined in Melampsora americana over two growing seasons via genotyping-by-sequencing to identify single-nucleotide polymorphism markers. In conjunction with this project, a reference genome of rust isolate R15-033-03 was generated to aid in variant discovery. Sampling between years allowed regional and site-specific investigation into population dynamics, in the context of both wild and cultivated hosts within high-density plantings. This work revealed that this pathogen is largely panmictic over the sampled areas, with few sites showing moderate genetic differentiation. These data support the hypothesis of sexual recombination between growing seasons because no genotype persisted across the two years of sampling. Additionally, clonality was determined as a driver of pathogen populations within cultivated fields and single shrubs; however, there is also evidence of high genetic diversity of rust isolates in all settings. This work provides a framework for M. americana population structure in the Great Lakes region, providing crucial information that can aid in future resistance breeding efforts.

Plant Sciences↗

Luteibacter mycovicinus sp. nov., a yellow-pigmented gammaproteobacterium found as an endohyphal symbiont of endophytic Ascomycota

We isolated and described a yellow-pigmented strain of bacteria (strain 9143 T ), originally characterized as an endohyphal inhabitant of an endophytic fungus in the Ascomycota. Although the full-length sequence of its 16S rRNA gene displays 99 % similarity to Luteibacter pinisoli, genomic hybridization demonstrated <30 % genomic similarity between 9143 T and its closest named relatives, further supported by average nucleotide identity results. This and related endohyphal strains form a well-supported clade separate from L. pinisoli and other validly named species including the most closely related Luteibacter rhizovicinus. The name Luteibacter mycovicinus sp. nov. is proposed, with type strain 9143 T (isolate DBL433), for which a genome has been sequenced and is publicly available from the American Type Culture Collection (ATCC TSD-257 T ) and from the Leibniz Institute DSMZ (DSM 112764 T ). The type strain reliably forms yellow colonies across diverse media and growth conditions (lysogeny broth agar, King’s Medium B, potato dextrose agar, trypticase soy agar and Reasoner's 2A (R2A) agar). It forms colonies readily at 27 °C on agar with a pH of 6–8, and on salt (NaCl) concentrations up to 2 %. It lacks the ability to utilize sulphate as a sulphur source and thus only forms colonies on minimal media if supplemented with alternative sulphur sources. It is catalase-positive and oxidase-negative. Although it exhibits a single polar flagellum, motility was only clearly visible on R2A agar. Its host range and close relatives, which share the endohyphal lifestyle, are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation

The genusCatenibacillus(familyLachnospiraceae, phylumBacillota) includes only one cultivated species so far,Catenibacillus scindens,isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinalCatenibacillusstrain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designatedCatenibacillus decagia, and showed its ability to deglycosylateC-coupled flavone and xanthone glucosides andO-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome ofC. scindensand ten faecal metagenome-assembled genomes assigned to the genusCatenibacillus, we performed a comparative genome analysis and searched for genes encoding potentialC-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism ofCatenibacillusstrains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. BothC. scindensandC. decagiaencode a flavonoidO-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoidC-deglycosylation system ofDoreastrain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required forC-deglycosylation. The diversity ofdgpAanddgpBCgene clusters might explain the broadC-glycoside substrate spectrum ofC. scindensandC. decagia. The otherCatenibacillusgenomes encode only a few potential flavonoid-converting enzymes. Our results indicate that severalCatenibacillusspecies are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.

Genetics & Heredity↗

Genomic reconstruction of Bacillus anthracis from complex environmental samples enables high-throughput identification and lineage assignment in Pakistan

Bacillus anthracis, the causative agent of anthrax, is a highly virulent zoonotic pathogen primarily affecting domesticated and wild herbivores. Human exposure to B. anthracis is primarily through contact with infected animals or contaminated animal products. In Pakistan, where livestock vaccines are largely unavailable and infected carcasses are often disposed of improperly, the risk to humans, wildlife and livestock is significant. Currently, the diagnosis of anthrax infections and outbreak tracing necessitates the isolation and culturing of B. anthracis, a process that requires BSL-3 facilities. In this study, we show that positive identification, genome reconstruction and lineage assignment can be accomplished using bioinformatic analysis of DNA extracted directly from environmental samples that would otherwise provide the starting material for isolation and culturing. This approach does not require laboratory target enrichment as is necessary for other pathogens, due in part to the extremely high bacterial load in the bloodstream in the deceased animals. Using these methods, we greatly expand the knowledge of endemic B. anthracis in Pakistan. We provide the first reference B. anthracis genomes from Pakistan since the 1970s and identify A.Br.014 Aust94 as a minor circulating sublineage alongside the dominant A.Br.047 Vollum. Future work will focus on the limits of detection and will determine if this bioinformatic method can be expanded more broadly for B. anthracis or other pathogens to replace typical culture-based methods.

A.Br.047 Vollum↗

Genomic analysis of Klebsiella aerogenes circulating in New Mexico

Klebsiella aerogenes is an opportunistic pathogen and a growing cause of healthcare-associated infections, characterized by multidrug resistance and the emergence of global high-risk clones. However, regional genomic surveillance data remain limited. Here, we sought to characterize the population structure, transmission dynamics and resistance mechanisms of clinical K. aerogenes in Albuquerque, New Mexico. We sequenced 177 clinical isolates collected between 2021 and 2023. We also developed a novel, species-specific PopPUNK database to facilitate rapid, high-resolution typing. The New Mexico K. aerogenes population was diverse but dominated by two global pandemic lineages, ST93 (47.5%) and ST4 (7.9%), which were significantly enriched for the virulence factors yersiniabactin and colibactin. Genomic evidence for recent local transmission was rare, with only four putative transmission pairs identified. The resistome was characterized by intrinsic and adaptive mutations. Nearly all isolates possessed gyrA mutations associated with decreased fluoroquinolone susceptibility. Mutations in the AmpC regulator AmpD and the outer membrane porin Omp36 were common, particularly within the dominant ST93 lineage. These mutations have been associated with increased AmpC-mediated carbapenem resistance. Our findings underscore the critical importance of genomic surveillance to monitor the transmission and evolution of adaptive resistance.

59 BASIC BIOLOGICAL SCIENCES↗

Understanding Majorana braiding in superconductors with a fixed total number of particles

Mean-field one-dimensional topological superconductors host edge Majorana zero modes (MZMs) that encode a topologically protected ground-state degeneracy and enable robust braiding operations within this subspace. Mean-field states lack definite particle number and thus cannot represent isolated systems. Nevertheless, projecting them onto fixed particle number can yield good approximations to an isolated superconductor ground state. In earlier work [Sajith et al., Phys. Rev. B 109, 184509 (2024)] we showed that the projected Kitaev wave function of a single wire preserves some important mean-field features, such as the zero-energy spectral peaks near the wire edges. However, uniqueness of the fixed-number ground state does not allow for any nontrivial operations in the ground-state subspace. To overcome this limitation, here we consider the case of multiple wires with a conserved total charge, using the same approach. In the limit of vanishing interwire coupling, this system has a macroscopic ground-state degeneracy. We show how this degeneracy is resolved by coherent single-particle tunneling, and identify special many-body states which play the same role as the MZM parity states in the mean field. In this work, we demonstrate how braiding operations can be implemented and discuss both intrinsic and extrinsic limits on their fidelity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Localized triplons and site stuffing in the quantum dimer magnet BiYbGeO5

Thermodynamic and muon spin relaxation measurements have recently highlighted BiYbGeO5 as a new example of a rare-earth-based quantum dimer magnet with isolated Yb3+ spin-1/2 dimers. However, direct spectroscopic evidence of the triplet excitations and measurements of the structural disorder are lacking. In this work, polycrystalline BiYbGeO5 was synthesized using conventional high-temperature solid-state methods and investigated via high-resolution neutron powder diffraction and inelastic neutron scattering. Diffraction measurements down to 58 mK reveal no signatures of magnetic order and indicate that nearly 20% of Yb3+ sites are replaced by nonmagnetic Bi3+, introducing significant structural disorder. Inelastic neutron scattering shows dispersionless triplon excitations, consistent with localized, noninteracting spin dimers. Fits to the triplet excitation spectrum with an XXZ-type anisotropic exchange give 𝐽XX=0.100⁢(1)⁢meV and 𝐽Z=0.202⁢(1)⁢meV. These findings establish BiYbGeO5 as a structurally disordered but magnetically well-isolated quantum dimer system, providing a model platform for studying the resilience of entangled spin states to site dilution.

Kapoor, Rachit [Brock University, Canada]↗

Carbon complexes in highly C-doped GaN

We investigate the properties of heavily C-doped GaN grown by hydride vapor phase epitaxy using both optical experiments and hybrid density functional theory calculations. Previous work has established that carbon acceptors (C N ) give rise to a yellow luminescence band near 2.2 eV along with a blue luminescence band near 2.9 eV. Photoluminescence measurements show the yellow band shifting as a function of carbon concentration, suggesting a change in the behavior of carbon species as carbon content increases. With hybrid density functional theory we calculate the electrical and optical behavior of carbon centers containing multiple carbon impurities, which may arise in heavily doped material. We compare the behavior of these complexes to the isolated centers, and find that the dicarbon donor-acceptor (C Ga –C N ) complex is a candidate to explain the shift in the yellow luminescence peak. Tricarbon complexes have high formation energies and modest binding energies, and also give rise to optical transitions that are inconsistent with the observed spectra. We also identify the split dicarbon interstitial on the gallium site as a low-energy species with a large binding energy that may act to compensate carbon acceptors. Here, local vibrational modes are calculated for carbon impurity centers, and we compare these results to recent experiments. Dicarbon and tricarbon complexes involving C Ga and C N exhibit modes that are only slightly higher than the isolated species, while carbon interstitials and related complexes give rise to vibrational modes much higher than C Ga and C N .

36 MATERIALS SCIENCE↗

Local site behavior of the 5$d$ and 4$f$ ions in the frustrated pyrochlore Ho 2 Os 2 O 7

The pyrochlore osmate Ho 2 Os 2 O 7 is a candidate material for a fragile J=0 local singlet ground state, however little is known regarding the single-ion behavior of either the Os or Ho ions. To address this we present polarized neutron powder diffraction (PNPD) and resonant inelastic x-ray scattering (RIXS) measurements that separately probe the local site behavior of the Os and Ho ions. The PNPD results are dominated by Ho 3+ scattering and the analysis reveals local site susceptibility behavior consistent with spin ice materials. Complimentary unpolarized neutron powder diffraction show an ordered spin ice ground state in an applied magnetic field. To isolate the Os 4+ single-ion behavior we present resonant inelastic x-ray scattering (RIXS) measurements at the osmium L-edge. Analysis of the RIXS spectra parameterize the spin-orbit coupling (0.35 eV), Hund’s coupling (0.27 eV) and trigonal distortion (-0.17 eV). Here, the results are considered within the context of a J=0 model and possible departures from this through structural distortions, excitonic interactions and 5d-4f interactions between the Os ion and the surrounding Ho lattice. The experimental methodology employed highlights the complimentary information available in rare earth based 5d pyrochlores from distinct neutron and x-ray scattering techniques that allow for the isolation and determination of the behavior of the different ions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Highly tunable magnetocrystalline anisotropy energy in Fe3+-doped BaTiO3

Magnetic dopants in ferroelectric oxide host materials provide a platform for electric field control of isolated spins, facilitated by tuning of the magnetocrystalline anisotropy energy (MCAE). We present first-principles calculations of the MCAE experienced by isolated Fe3+ dopants in the tetragonal, orthorhombic, and rhombohedral phases of the prototypical ferroelectric BaTiO3. We identify an order-of-magnitude decrease in the MCAE in the rhombohedral phase relative to the tetragonal and orthorhombic phases. We explain this dramatic decrease, as well as the formation of a spin-easy plane in the tetragonal phase and spin-easy axes in the orthorhombic and rhombohedral phases, using crystal field theory arguments. Building a superposition model from crystal field theory, we show how a set of simple criteria based on crystalline environment can be used to estimate the MCAE. We suggest this as a route to rapidly screen candidate ferroelectric hosts and magnetic dopants that possess phases with spin-easy axes and maximal MCAE tunability.

Barker, Bradford A↗

Experimental studies of the two-step scheme with an intense radioactive 132 Sn beam for next-generation production of very neutron-rich nuclei

The study of nuclei in the yet-unexplored, very neutron-rich, mid- to heavy-mass region of the nuclear chart, comprising perhaps half of all nuclei predicted to exist, is leading to new and/or upgraded facilities, as well as to research into the underlying production processes. In the present study, the usefulness of the two-step scheme, an alternate method to produce very neutron-rich nuclei, by a combination of an isotope-separation online (ISOL) system as a first step, and in-beam fragmentation of re-accelerated radioactive isotopes (RIs) as a second step, was investigated with a 132 Sn beam. In this work, very neutron-rich RIs around the neutron-rich neutron number N = 82 region were produced from the 278-MeV/nucleon 132 Sn beam impinging on a 5.97-mm Be target, and their production cross sections were measured. Yields were then estimated for the two-step scheme with the 132 Sn beam relative to the ones by a one-step scheme, in-flight fission of a 238 U beam, for 1-MW proton and 238 U beams at respective RI-beam facilities. This comparison suggests that the two-step scheme with the 132 Sn beam provides yields >40-times higher than those with the one-step scheme for the very neutron-rich N = 82 region. Moreover, by using various RI beams over the nuclear chart from ISOL, certain kinds of very neutron-rich RIs around the supernova r-process path can be produced with greater yields than by the one-step approach.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Short-range correlation physics at low renormalization group resolution

Recent experiments have succeeded in isolating processes for which short-range correlation (SRC) physics is dominant and well accounted for by SRC phenomenology. But an alternative and compelling picture emerges from renormalization group (RG) evolution to low RG resolution. At high RG resolution, SRCs are identified as components in the nuclear wave function with relative pair momenta greater than the Fermi momentum. Scale separation results in wave-function factorization that can be exploited with phenomenologies such as the generalized contact formalism or the low-order correlation operator approximation. Evolution to lower resolution shifts SRC physics from nuclear structure to the reaction operators without changing the measured observables. We show how the features of SRC phenomenology manifested at high RG resolution are cleanly identified at low RG resolution using simple two-body operators and local-density approximations with uncorrelated wave functions, all of which can be systematically generalized. We verify that the experimental consequences to date follow directly at low resolution from well-established properties of nucleon-nucleon interactions such as the tensor force. Thus the RG reconciles the contrasting pictures of the same experiment and shows how to get correct results using wave functions without SRC components. Finally, our demonstration has implications for the analysis of knockout reactions for which SRC physics is not cleanly isolated.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Laboratory electron screening in nuclear resonance reactions

Both nonresonant and resonance reaction data are subject to laboratory electron screening effects. For non resonant reactions, such effects are well documented and the measured cross sections can be corrected to find the unscreened ones. Frequently, the procedure and expression to calculate laboratory electron screening factors for nonresonant reactions are also applied to isolated narrow resonances, without much theoretical support or experimental evidence. Here, a simple model is applied to estimate electron screening factors, lengths, and potentials for narrow resonances. The corrections to the measured data result in an enhancement of the unscreened resonance strengths by less than 0.2%, contrary to published narrow-resonance screening correction factors, which predict a reduction of the unscreened strengths by up to 25%. Unless it can be proven otherwise, it is recommended that measured strengths of isolated narrow resonances not be corrected for laboratory electron screening. The prospects of investigating laboratory electron screening effects by measuring almost negligible differences in resonance strengths are not promising. Instead, the difference of the resonance energy for the unscreened and screened situation may be measurable. As an example, the case of the E r = 956-keV resonance in the 27 Al(p,γ) 28 Si reaction is discussed. It is also demonstrated that the claim of a previously reported detection of a resonance near 800 keV in the 176 Lu(p,n) 176 Hf reaction is incorrect.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Comparison of transverse single-spin asymmetries for forward π 0 production in polarized pp , p Al and p Au collisions at nucleon pair c.m. energy √sNN=200 GeV

The STAR collaboration reports a measurement of the transverse single-spin asymmetries, A N , for neutral pions produced in polarized proton collisions with protons ( p p ), with aluminum nuclei ( p Al ) and with gold nuclei ( p Au ) at a nucleon-nucleon center-of-mass energy of 200 GeV. Neutral pions are observed in the forward direction relative to the transversely polarized proton beam, in the pseudorapidity region 2.7 < η < 3.8 . Results are presented for π 0 s observed in the STAR forward meson spectrometer electromagnetic calorimeter in narrow Feynman x ( x F ) and transverse momentum ( p T ) bins, spanning the range 0.17 < x F < 0.81 and 1.7 < p T < 6.0 GeV / c . For fixed x F < 0.47 , the asymmetries are found to rise with increasing transverse momentum. For larger x F , the asymmetry flattens or falls as p T increases. Parametrizing the ratio r ( A ) ≡ A N ( p A ) / A N ( p p ) = A P over the kinematic range, the ratio r ( A ) is found to depend only weakly on A , with ( P ) = - 0.027 ± 0.005 . No significant difference in P is observed between the low- p T region, p T < 2.5 GeV / c , where gluon saturation effects may play a role, and the high- p T region, p T > 2.5 GeV / c . It is further observed that the value of A N is significantly larger for events with a large- p T isolated π 0 than for events with a nonisolated π 0 accompanied by additional jetlike fragments. The nuclear dependence r ( A ) is similar for isolated and nonisolated π 0 events.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗