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For the Ta equation of state (EOS) model introduced in our recent publication (Gorman et al., 2023), we have made a fairly accurate analytic fit to this EOS over a limited range. The detailed functional form and associated parameters of this fit are presented here.
After successful fitting of prompt ν for 235 U, 238 U, and 239 Pu(n,f) using CGMF, we have moved on to the minor plutonium isotopes. Minor isotopes pose a greater challenge both because there is less data available and we do not, by default, have parametrizations in CGMF already. Initially, we had planned to mitigate these challenges—and provide consistency within CGMF—by taking a stepped approach to the optimization. Continuing from the 239 Pu work, we would then fit 241Pu(n,f) $\overline{ν}$, where there is also a number of experimental measurements, keeping consistency between the parameters that are included in the calculation for 239 Pu and 241 Pu. With these parametrizations settled, we could consistently optimize 240 Pu(n,f) $\overline{ν}$. Following that step, we would move on to 242 Pu(n,f) (and increasing neutron number) and 238 Pu(n,f) (and decreasing neutron number). By including the fissioning systems in this manner, we should be able to minimize the unknown parameters in CGMF. We were also able to develop systematics for the CGMF input parameters along the Pu isotopic chain. However, after studies in the beginning of FY23, where we found reasonable agreement between CGMF and experimental prompt neutron multiplicities for 238−242 Pu, using a compound mass dependent parametrization from, and from discussions with I. Stetcu and P. Talou, we instead performed the evaluation of all five isotopes simultaneously. For all parameters in CGMF, they are either the same for each compound nucleus, or have a dependence on the compound mass. The details of these updates are given in. This report builds upon those details. In this short report, we first give an example of how we have updated CGMF to include 240 Pu(n,f) and 242 Pu(n,f), keeping consistency with the current 239 Pu and 241 Pu calculations, but without rigorous optimization (Sec. 2). Then, we will show in Section 3 what experimental data exist for the various isotopes to provide some insight into why 241 Pu and 239 Pu are used as anchor points. The evaluation is detailed in Section 4, and the comparison between CGMF calculations using the evaluated parameters and other prompt observables besides average neutron multiplicity are discussed in Section 2.2. Finally, we present conclusions and future work in Section 5.
We developed a novel, high-throughput microfluidic device design containing “interaction zones” where progeny cell lines compete against each other allowing for accurate analysis of bacterial cell fitness. The goal of the project was to use the device for two applications: 1) gene knockout screening and 2) antibiotic resistance screening. The microfluidic platform was fabricated using photolithography and soft lithography in polydimethylsiloxane (PDMS). E.coli Keio mutants and fluorescent wildtype parent were chosen for the study. Cells were grown overnight and their loading into the devices and seeding in mother machines was optimized. For mutant screening, the least fit mutant and wildtype parent were cultured individually and then added to the microfluidic device. The mother machines which were seeded with mutant and wildtype were imaged through time lapse microscopy and the growth of cells was observed. For antibiotic screening, wildtype E.coli cells which were grown overnight were added to the device and washed with media containing the antibiotic ampicillin. The growth pattern in presence and absence of ampicillin was observed through time lapse microscopy. It was observed that over a period of four hours, both the mutant and the wildtype divided in the mother machine and pushed daughter cells out into the interaction zone. In case of the antibiotic screening experiment, the fluorescent wildtype divided both in the absence and presence of sublethal concentration of ampicillin. This study is a proof of concept demonstration of high- throughput single cell analysis of cells using a novel microfluidics device.
Light output response of scintillators is crucial to the utilization of organic scintillators as effective tools in radiation detection and measurement. While the response is a continuous distribution, the light output corresponding to the maximum energy deposition is crucial in effectively understanding and simulating a detector. There are a variety of fits derived in literature that will vary for every detector material. The Light Output Response Fitter, or LORF Program is a python script designed to easily and quickly compute and plot fits for a variety of scintillator light output models. It includes a stopping power library constructed from SRIM including Organic Glass, EJ309, EJ301, Stilbene, EJ276, and their deuterated counterparts by default, with the ability for the user to add custom stopping power libraries. The user is also capable of importing the python package and utilizing its in-built functions as appropriate. Uses for this capability include plotting and computing a model with known parameters.
More luminous Type Ia supernovae prefer less massive hosts and regions of higher star formation. This correlation is inverted during width–color–luminosity light-curve standardization resulting in step-like biases of distance measurements with respect to host properties. Using the PMAS/PPak Integral-field Supernovahosts COmpilation (PISCO) supernova host sample and Sloan Digital Sky Survey, Galaxy Evolution Explorer, and Two Micron All Sky Survey photometry, we compare host stellar mass and specific star-formation rate (sSFR) from different observation methods, including local versus global, and fitting techniques to measure their impact on the host step biases. Mass-step measurements for all our mass samples are consistent within a 1σ significance from –0.03 ± 0.02 mag to –0.04 ± 0.02 mag. Including or excluding UV information had no effect on measured mass-step size or location. sSFR step sizes are more significant than mass-step measurements and varied from 0.05 ± 0.03 mag (Hα) and 0.06 ± 0.02 mag (UV) for a 51 host sample. The sSFR step location is influenced by the mass sample used to normalize star formation and by sSFR tracer choice. The step size is reduced to 0.04 ± 0.03 mag when using all available 73 hosts with Hα measurements. This 73 PISCO host subsample overall lacked a clear step signal, but here we are searching for whether different choices of mass or sSFR estimation can create a step signal. We find no evidence that different observation or fitting techniques choices can create a distance measurement step in either mass or sSFR.
We present an autodifferentiable rejection sampling algorithm termed Rejection Sampling with Autodifferentiation (RSA). In conjunction with reweighting, we show that RSA can be used for efficient parameter estimation and model exploration. Additionally, this approach facilitates the use of unbinned machine-learning-based observables, allowing for more precise, data-driven fits. To showcase these capabilities, we apply an RSA-based parameter fit to a simplified hadronization model.
This paper introduces a novel track-length extension fitting algorithm for measuring the kinetic energies of inelastically interacting particles in liquid argon time projection chambers (LArTPCs). The algorithm finds the most probable offset in track length for a track-like object by comparing the measured ionization density as a function of position with a theoretical prediction of the energy loss as a function of the energy, including models of electron recombination and detector response. The algorithm can be used to measure the energies of particles that interact before they stop, such as charged pions that are absorbed by argon nuclei. The algorithm's energy measurement resolutions and fractional biases are presented as functions of particle kinetic energy and number of track hits using samples of stopping secondary charged pions in data collected by the ProtoDUNE-SP detector, and also in a detailed simulation. Additional studies describe the impact of the dE/dx model on energy measurement performance. The method described in this paper to characterize the energy measurement performance can be repeated in any LArTPC experiment using stopping secondary charged pions.
Abstract Variation in gene copy number can alter gene expression and influence downstream phenotypes; thus copy-number variation provides a route for rapid evolution if the benefits outweigh the cost. We recently showed that genetic background significantly influences how yeast cells respond to gene overexpression, revealing that the fitness costs of copy-number variation can vary substantially with genetic background in a common-garden environment. But the interplay between copy-number variation tolerance and environment remains unexplored on a genomic scale. Here, we measured the tolerance to gene overexpression in four genetically distinct Saccharomyces cerevisiae strains grown under sodium chloride stress. Overexpressed genes that are commonly deleterious during sodium chloride stress recapitulated those commonly deleterious under standard conditions. However, sodium chloride stress uncovered novel differences in strain responses to gene overexpression. West African strain NCYC3290 and North American oak isolate YPS128 are more sensitive to sodium chloride stress than vineyard BC187 and laboratory strain BY4743. Consistently, NCYC3290 and YPS128 showed the greatest sensitivities to overexpression of specific genes. Although most genes were deleterious, hundreds were beneficial when overexpressed—remarkably, most of these effects were strain specific. Few beneficial genes were shared between the sodium chloride-sensitive isolates, implicating mechanistic differences behind their sodium chloride sensitivity. Transcriptomic analysis suggested underlying vulnerabilities and tolerances across strains, and pointed to natural copy-number variation of a sodium export pump that likely contributes to strain-specific responses to overexpression of other genes. Our results reveal extensive strain-by-environment interactions in the response to gene copy-number variation, raising important implications for the accessibility of copy-number variation-dependent evolutionary routes under times of stress.
Despite advances in our understanding of bacterial plant colonization, the extent to which growth substrate influences the molecular mechanisms enabling bacteria to efficiently colonize plants remains poorly understood. To address this, we used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Paraburkholderia graminis OAS925, an efficient rhizosphere colonizer, and Brachypodium distachyon grown in six different substrates. Of the 382 rhizosphere colonization genes that we identified in OAS925, 348 genes (91.1%) are dependent on the growth substrate evaluated, and 34 genes (8.9%) are shared across all the substrates. Both the core and substrate-dependent colonization genes are from multiple functional categories, demonstrating the multifaceted and major impact that plant growth substrate has on bacterial colonization. The identified colonization genes and their varied importance across plant growth substrates could not be readily explained by differences in root exudate profiles, suggesting that the substrate environment itself plays an outsized role in the ability of a bacterium to colonize the rhizosphere. Our data confirm that bacterial fitness for plant colonization is strongly influenced by plant growth substrate type and highlights the importance of taking this parameter into consideration when engineering bacterial strains for improved host colonization.
An additional generation of quarks and leptons and their SUSY counterparts, which are vector-like under the Standard Model gauge group but are chiral with respect to the new U(1) 3–4 gauge symmetry, are added to the Minimal Supersymmetric Standard Model (MSSM). We show that this model is a GUT and unifies the three SM gauge couplings and also the additional U(1) 3–4 coupling at a GUT scale of ≈ 5 × 10 16 GeV and explains the experimentally observed deviation of the muon g – 2. We also fit the quark flavor changing processes consistent with the latest experimental data and look at the effect of the new particles on the W boson mass without obviously conflicting with the observed masses of particles, CKM matrix elements, neutrino mixing angles, their mass differences, and the lepton-flavor violating bounds. This model predicts sparticle masses less than 25 TeV, with a gluino mass ≈ 2.3 – 3 TeV consistent with constraints, and one of the neutralinos as the LSP with a mass of ≈ 480 – 580 GeV, which is a potential dark matter candidate. The model is string theory motivated and predicts the VL quarks, leptons, a massive Z' and two Dirac neutrinos at the TeV scale and the branching ratios of μ → eγ, τ → μγ and τ → 3μ with BR(μ → eγ) within reach of future experiments.
Effective field theory tools are essential for exploring non-Standard Model physics at the LHC in the absence of the discovery of new light particles. Predictions for observables are typically made at the lowest order in the QCD and electroweak expansions in the Standard Model effective field theory (SMEFT) and often ignore the effects of flavor. Here, we present results for electroweak precision observables (EWPOs) at the next-to-leading order QCD and electroweak expansions (NLO) of the SMEFT with an arbitrary flavor structure for the fermion operators. Numerical NLO SMEFT fits to EWPOs have a strong dependence on the assumed flavor structures and we demonstrate this using various popular assumptions for flavor symmetries.
According to the good genes and genetic compatibility hypotheses, females of socially monogamous species obtain genetic benefits for their offspring by performing extrapair copulations with males of higher quality than their social mates or males with whom they are more genetically compatible. If extrapair offspring do receive genetic benefits in the form of advantageous alleles or more compatible allele combinations, they should outperform their within-pair half-siblings' survival and/or reproductive output. Here, in this study, we followed 52 extrapair and 737 within-pair blue-footed booby, Sula nebouxii, offspring during their first 10 years of life (excluding the embryonic period and the first 10 days after hatching) to assess whether they differed in fledging probability, fledgling body condition, recruitment probability, age at first reproduction, number of breeding events or accumulated breeding success. Extrapair and within-pair offspring did not differ in any of these proxies of fitness. Furthermore, we found that extrapair offspring were equally likely to occur in any hatching position. However, differences in fledgling production over the lifetime could not be ruled out, and because only within-pair production of eggs and fledglings was tallied, the possibility remains that extrapair offspring could produce more extrapair offspring later in life than do within-pair offspring. Furthermore, the possibility of context-dependent genetic benefits occurring only under stressful conditions cannot be discounted because our sample of offspring was obtained in a single exceptionally favourable reproductive season.
Bioconversion of lignin-related aromatic compounds relies on robust catabolic pathways in microbes. Sphingobium sp. SYK-6 (SYK-6) is a well-characterized aromatic catabolic organism that has served as a model for microbial lignin conversion, and its utility as a biocatalyst could potentially be further improved by genome-wide metabolic analyses. To this end, we generate a randomly barcoded transposon insertion mutant (RB-TnSeq) library to study gene function in SYK-6. The library is enriched under dozens of enrichment conditions to quantify gene fitness. Several known aromatic catabolic pathways are confirmed, and RB-TnSeq affords additional detail on the genome-wide effects of each enrichment condition. Selected genes are further examined in SYK-6 or Pseudomonas putida KT2440, leading to the identification of new gene functions. The findings from this study further elucidate the metabolism of SYK-6, while also providing targets for future metabolic engineering in this organism or other hosts for the biological valorization of lignin.
The widespread application of genetically modified microorganisms (GMMs) across diverse sectors underscores the pressing need for robust strategies to mitigate the risks associated with their potential uncontrolled escape. This study merges computational modeling with CRISPR interference (CRISPRi) to refine GMM metabolic robustness. Utilizing ensemble modeling, we achieved high-throughput in silico screening for enzymatic targets susceptible to expression alterations. Translating these insights, we developed functional CRISPRi, boosting fitness control via multiplexed gene knockdown. Our method, enhanced by an insulator-improved gRNA structure and an off-switch circuit controlling a compact Cas12m, resulted in rationally engineered strains with escape frequencies below National Institutes of Health standards. The effectiveness of this approach was confirmed under various conditions, showcasing its ability for secure GMM management. This research underscores the resilience of microbial metabolism, strategically modifying key nodes to halt growth without provoking significant resistance, thereby enabling more reliable and precise GMM control. A record of this paper's transparent peer review process is included in the supplemental information.
In this work we describe a method to automatically generate an ion implantation recipe, a set of energies and fluences, to produce a desired defect density profile in a solid using the fewest required energies. We simulate defect density profiles for a range of ion energies, fit them with an appropriate function, and interpolate to yield defect density profiles at arbitrary ion energies. Given Ν energies, we then optimize a set of Ν energy-fluence pairs to match a given target defect density profile. Finally, we find the minimum Ν such that the error between the target defect density profile and the defect density profile generated by the Ν energy-fluence pairs is less than a given threshold. Inspired by quantum sensing applications with nitrogen-vacancy centers in diamond, we apply our technique to calculate optimal ion implantation recipes to create uniform-density 1 μm surface layers of 15 N or vacancies (using 4 He).
In this work, the density fitting (DF) approximation is added to the restricted Hartree–Fock (RHF) implementation in the JuliaChem computational chemistry code. Utilizing a DF algorithm that uses symmetry and integral screening, a significant reduction in time to compute the Fock matrix is achieved. The symmetry and screening DF-RHF techniques were adapted to be performed on graphics processing units (GPUs), which are well suited to perform the matrix multiplications that comprise the bulk of the Fock build time in DF-RHF. The JuliaChem DF-RHF GPU algorithm employs a novel approach that automatically switches between two DF-RHF algorithms depending on the number of basis functions in the calculation. The JuliaChem GPU DF-RHF implementation demonstrates up to 2× speedup for Fock build times compared to the existing best-in-class GPU DF-RHF implementation by operating directly on screened intermediate matrices. Due to the high portability of the Julia language code, the JuliaChem CPU and GPU DF-RHF implementations could be benchmarked on a variety of CPU and GPU architectures from multiple hardware vendors.
We provide a strategy to optimize density functional tight-binding (DFTB) parameterization for the calculation of the structures and properties of organic molecules consisting of hydrogen, carbon, nitrogen, and oxygen. We utilize an objective function based on similarity measurements and the Particle Swarm Optimization (PSO) method to find an optimal set of parameters. This objective function considers not only the common DFTB descriptors of binding energies and atomic forces but also incorporates relative energies of isomers into the fitting procedure for more chemistry-driven results. The quality in the description of the binding energies and atomic forces is measured based on the Ballester similarity index and relative energies through a similarity index induced by the Levenshtein edit distance to quantify the correct energetic order of isomers. Training and testing datasets were created to include all relevant chemical functional groups. Finally, the accuracy of this strategy is assessed, and its range of applicability is discussed by comparison against our previous parameterization. The improved performance of the new DFTB parameterization is validated with respect to the density functional theory large datasets QM-9 and ANI-1, where excellent agreement is found between the structures and properties available in these datasets, and the ones obtained with DFTB.
The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives–3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)–the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.