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The main protease (M pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics.
An ab initio approach describes the main and satellite features of the Fe 2p XPS of Fe 2 O 3 and shows their origin in terms of normal and shake configurations.
Galaxy evolution has been studied by interpreting the spectral energy distribution of galaxies using spectral synthesis codes. This method has been crucial in discovering different pillars of modern galaxy evolution theories. However, this analysis was mostly carried out using spectral synthesis codes that are purely stellar, that is, they assume that the nebular contribution to the total continuum is negligible. The code FADO is the first publicly available population spectral synthesis tool that treats the contribution from ionised gas to the observed emission self-consistently. This is expected to have a particularly strong effect in star-forming (SF) galaxies. We study the impact of the nebular contribution on the determination of the star formation rate (SFR), stellar mass, and consequent effect on the star-forming main sequence (SFMS) at low redshift. We applied FADO to the spectral database of the SDSS to derive the physical properties of galaxies. As a comparison, we used the data in the MPA-JHU catalogue, which contains the properties of SDSS galaxies derived without the nebular contribution. We selected a sample of SF galaxies with Hα and Hβ flux measurements, and we corrected the fluxes for the nebular extinction through the Balmer decrement. We then calculated the Hα luminosity to estimate the SFR. Then, by combining the stellar mass and SFR estimates from FADO and MPA-JHU, the SFMS was obtained. The Hα flux estimates are similar between FADO and MPA-JHU. Because the Hα flux was used as tracer of the SFR, FADO and MPA-JHU agree in their SFR. The stellar mass estimates are slightly higher for FADO than for MPA-JHU on average. However, considering the uncertainties, the differences are negligible. With similar SFR and stellar mass estimates, the derived SFMS is also similar between FADO and MPA-JHU. Our results show that for SDSS normal SF galaxies, the additional modelling of the nebular contribution does not affect the retrieved fluxes and consequentially also does not influence SFR estimators based on the extinction-corrected Hα luminosity. For the stellar masses, the results point to the same conclusion. These results are a consequence of the fact that the vast majority of normal SF galaxies in the SDSS have a low nebular contribution. However, the obtained agreement might only hold for local SF galaxies, but higher-redshift galaxies might show different physical properties when FADO is used. This would then be an effect of the expected increased nebular contribution.
Understanding impurity transport in tokamak plasmas is crucial to control radiative losses and material migration in future magnetic fusion reactors. In this work we deploy the SolEdge2D-EIRENE code to model the boundary plasma in a WEST discharge, satisfactorily reproducing measurements of both upstream and divertor plasma conditions. Additionally, the spatial distribution of oxygen, studied here as a representative light impurity, is compared to vacuum ultraviolet spectroscopy measurements acquired with an oscillating line of sight. The simulation captures a key feature of the experiment, namely a factor of sime2 higher oxygen brightness in the inner divertor region compared to the outer one. This spatial asymmetry in oxygen concentration is interpreted by analyzing the balance of friction forces and thermal gradient forces that the light impurity exchanges with the main plasma.
ABSTRACT We evaluate the impact of imaging systematics on the clustering of luminous red galaxies (LRG), emission-line galaxies (ELG), and quasars (QSO) targeted for the upcoming Dark Energy Spectroscopic Instrument (DESI) survey. Using Data Release 7 of the DECam Legacy Survey, we study the effects of astrophysical foregrounds, stellar contamination, differences between north galactic cap and south galactic cap measurements, and variations in imaging depth, stellar density, galactic extinction, seeing, airmass, sky brightness, and exposure time before presenting survey masks and weights to mitigate these effects. With our sanitized samples in hand, we conduct a preliminary analysis of the clustering amplitude and evolution of the DESI main targets. From measurements of the angular correlation functions, we determine power law fits $r_0 = 7.78 \pm 0.26\, h^{-1}$Mpc, γ = 1.98 ± 0.02 for LRGs and $r_0 = 5.45 \pm 0.1\, h^{-1}$Mpc, γ = 1.54 ± 0.01 for ELGs. Additionally, from the angular power spectra, we measure the linear biases and model the scale-dependent biases in the weakly non-linear regime. Both sets of clustering measurements show good agreement with survey requirements for LRGs and ELGs, attesting that these samples will enable DESI to achieve precise cosmological constraints. We also present clustering as a function of magnitude, use cross-correlations with external spectroscopy to infer dN/dz and measure clustering as a function of luminosity, and probe higher order clustering statistics through counts-in-cells moments.
ABSTRACT Asteroseismology is a powerful tool to infer fundamental stellar properties. The use of these asteroseismic-inferred properties in a growing number of astrophysical contexts makes it vital to understand their accuracy. Consequently, we performed a hare-and-hounds exercise where the hares simulated data for six artificial main-sequence stars and the hounds inferred their properties based on different inference procedures. To mimic a pipeline such as that planned for the PLATO mission, all hounds used the same model grid. Some stars were simulated using the physics adopted in the grid, others a different one. The maximum relative differences found (in absolute value) between the inferred and true values of the mass, radius, and age were 4.32, 1.33, and 11.25 per cent, respectively. The largest systematic differences in radius and age were found for a star simulated assuming gravitational settling, not accounted for in the model grid, with biases of −0.88 per cent (radius) and 8.66 per cent (age). For the mass, the most significant bias (−3.16 per cent) was found for a star with a helium enrichment ratio outside the grid range. Moreover, an ∼7 per cent dispersion in age was found when adopting different prescriptions for the surface corrections or shifting the classical observations by ±1σ. The choice of the relative weight given to the classical and seismic constraints also impacted significantly the accuracy and precision of the results. Interestingly, only a few frequencies were required to achieve accurate results on the mass and radius. For the age the same was true when at least one l = 2 mode was considered.
ABSTRACT It has long been speculated that jet feedback from accretion on to the companion during a common envelope (CE) event could affect the orbital evolution and envelope unbinding process. We present global 3D hydrodynamical simulations of CE evolution (CEE) that include a jet subgrid model and compare them with an otherwise identical model without a jet. Our binary consists of a 2-M⊙ red giant branch primary and a 1- or 0.5-M⊙ main sequence (MS) or white dwarf (WD) secondary companion modelled as a point particle. We run the simulations for 10 orbits (40 d). Our jet model adds mass at a constant rate $\dot{M}_\mathrm{j}$ of the order of the Eddington rate, with maximum velocity vj of the order of the escape speed, to two spherical sectors with the jet axis perpendicular to the orbital plane. We explore the influence of the jet on orbital evolution, envelope morphology and envelope unbinding, and assess the dependence of the results on the jet mass-loss rate, launch speed, companion mass, opening angle, and accretion rate. In line with our theoretical estimates, jets are choked around the time of first periastron passage and remain choked thereafter. Subsequent to choking, but not before, jets efficiently transfer energy to bound envelope material. This leads to increases in unbound mass of up to $\sim 10{{\ \rm per\ cent}}$, as compared to the simulations without jets. We also estimate the cumulative effects of jets over a full CE phase, finding that jets launched by MS and WD companions are unlikely to dominate envelope unbinding.
The International Linear Collider (ILC) main linac comprises a series of 12 m-long cryomodules. The cryomodule contains eight 9-cell superconducting (SC) RF (SRF) cavities and an SC quadrupole magnet combined with dipole correctors to focus and steer electron and positron beams. The magnets are installed between the SRF cavity string and at the longitudinal center of a common cryomodule/cryostat. These magnets are conductively cooled by pure aluminum channels thermally connected to a 2 K two-phase helium pipe for cooling the SRF cavities. A recent study shows that field-emitted electrons, so-called “dark current” initiated in the SRF cavities, are transmitted through the SRF cavity string and reach the SC magnet. The energy is inevitably absorbed in the SC coil due to the magnetic field, resulting in risks of a quench caused by the coil heating. We are investigating alternate magnet designs by using Nb $_{3}$ Sn or $\text{MgB}_{2}$ SC and by adding the dark current absorber surrounding the beam-pipe to realize sustainable magnet operation under the dark current heating. We report the design study of the magnet system and interfaces to the cryomodule accommodating it with the SRF cavities.
Radio Frequency superconductivity has been a mainstay of accelerator science for decades. However, its benefits have yet to be applied to proton synchrotrons with demanding tuning requirements. For example, the Main Injector (MI), Fermilab's high-energy proton synchrotron, currently utilizes 20+ ferrite-loaded cavities for a targeted 1.2 s acceleration cycle. Harnessing the extremely high gradients associated with superconductivity, the required number of cavities could be reduced by an order of magnitude, dramatically lowering operational power requirements even with cryogenic considerations. Additionally, the current plans for the Fermilab accelerator complex evolution initiative involve almost doubling the number of cavities in MI if the same designs are to be used, further highlighting the potential benefits of superconductivity. These advantages are attractive, but to date, no tunable superconducting cavity suitable for MI has been proposed due to the incompatibility of conventional broadband tuning methods with superconductivity. Here, we present a tunable superconducting cavity concept capable of record-breaking performance. Tuning will be accomplished by using high-speed linear actuators to vary the insertion depth of metallic plungers into the cavity volume. This tuning concept is theoretically viable with currently available technology and will be fully compatible with a superconducting cavity.
There is an urgent need to repurpose drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent computational-experimental screenings have identified several existing drugs that could serve as effective inhibitors of the virus’ main protease, M pro , which is involved in gene expression and replication. Among these, ebselen (2-phenyl-1,2-benzoselenazol-3-one) appears to be particularly promising. Here, we examine, at a molecular level, the potential of ebselen to decrease Mpro activity. We find that it exhibits a distinct affinity for the catalytic region. Our results reveal a higher-affinity, previously unknown binding site localized between the II and III domains of the protein. A detailed strain analysis indicates that, on such a site, ebselen exerts a pronounced allosteric effect that regulates catalytic site access through surface-loop interactions, thereby inducing a reconfiguration of water hotspots. Together, these findings highlight the promise of ebselen as a repurposed drug against SARS-CoV-2.
Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M pro ) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 M pro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.
Two new structures of the N-terminal domain of the main replication protein, NS1, of human parvovirus B19 (B19V) are presented here. This domain (NS1-nuc) plays an important role in the “rolling hairpin” replication of the single-stranded B19V DNA genome, recognizing origin of replication sequences in double-stranded DNA, and cleaving (i.e., nicking) single-stranded DNA at a nearby site known as the terminal resolution site (trs). The three-dimensional structure of NS1-nuc is well conserved between the two forms, as well as with a previously solved structure of a sequence variant of the same domain; however, it is shown here at a significantly higher resolution (2.4 Å). Using structures of NS1-nuc homologues bound to single- and double-stranded DNA, models for DNA recognition and nicking by B19V NS1-nuc are presented that predict residues important for DNA cleavage and for sequence-specific recognition at the viral origin of replication.
Recent wildfires near vineyards in the Pacific United States have caused devastating financial losses due to smoke taint in wine. When wine grapes (Vitis vinifera) are exposed to wildfire smoke, their berries absorb volatile phenols derived from the lignin of burning plant material. Volatile phenols are released during the winemaking process giving the finished wine an unpleasant, smokey, and ashy taste known as smoke taint. Bacteria are capable of undergoing a wide variety of metabolic processes and therefore present great potential for bioremediation applications in many industries. In this study, we identify two strains of the same species that colonize the grape phyllosphere and are able to degrade guaiacol, a main volatile phenol responsible for smoke taint in wine. We identify the suite of genes that enable guaiacol degradation in Gordonia alkanivorans via RNAseq of cells growing on guaiacol as a sole carbon source. Additionally, we knockout guaA, a cytochrome P450 gene involved in the conversion of guaiacol to catechol; ΔguaA cells cannot catabolize guaiacol in vitro, providing evidence that GuaA is necessary for this process. Furthermore, we analyze the microbiome of berries and leaves exposed to smoke in the vineyard to investigate the impact of smoke on the grape microbial community. We found smoke has a significant but small effect on the microbial community, leading to an enrichment of several genera belonging to the Bacilli class. Collectively, this research shows that studying microbes and their enzymes has the potential to identify novel tools for alleviating smoke taint.
This is the FLUXNET-CH4 version of the carbon flux data for the site US-Ho1 Howland Forest (main tower).
The current program at Fermilab involves the construction of a new superconducting linear accelerator (LINAC) to replace the existing warm version. The new LINAC, together with other planned improvements, is in support of proton beam intensities in the Main Injector (MI) that will exceed 2 MW. Measuring the transverse profiles of these high intensity beams in a ring requires non-invasive techniques. The MI uses ionization profile monitors as its only profile system. An alternative technique involves measuring the deflection of a probe beam of electrons with a trajectory perpendicular to the proton beam. This type of device was installed in MI and initial studies of it have been previously presented. This paper will present the status and recent studies of the device utilizing different techniques.
A superconducting rf (SRF) cryomodule for International Linear Collider(ILC) Main Linac equips focus/steering magnets. The magnets are "superferric" magnets with four superconducting (SC) race track coils conductively cooled from the cryomodule LHe supply pipe. The quadrupole field gradient and dipole field are 40 T/m and 0.1 T, respectively. The magnet length and iron-pole radius are 1 m and 0.045 m, respectively. It is known that dark current is generated at SRF cavities and accelerated through the following linac string. The dark current reaches and heats the SC magnets. It is estimated that the power deposition in the magnet may reach more than a few watts and temperature of the SC coils may locally reach to critical temperature of NbTi. It is important to make the magnet not reach quench with sufficient conduction cooling. We aim to realize the SC magnet which can stably operate under such condition. We plan to develop test coils made of three types of SC materials, NbTi, Nb₃Sn, and MgB₂ and study thermal characteristics and stability . We will develop a short model magnet, based on the test coil results. Here, we will present the magnet design study and the R&D plan.
This work presents techniques for non-invasive transverse profile measurements of high-intensity proton beams using an Electron Beam Profile Scanner (EBPS). The EBPS utilizes low-energy electrons as a probe to analyze the transverse size of proton beams, allowing for potential analysis on a single-bunch basis. Recent upgrades to the Fermilab Main Injector have enhanced beam power on target to 1 MW, with future developments targeting 2 MW. The higher beam power has increased the demand for non-invasive diagnostics, as invasive methods can disrupt operations.The techniques presented include 1) the slow scan technique, which serves as a proof of concept for the probe beam, 2) the one-shot scan technique for measuring horizontal beam profiles, and 3) the raster scan technique for analyzing horizontal beam profiles as a function of the longitudinal distribution of the beam. The profiles obtained will be crucial for studying and understanding instabilities in high-power, high-intensity proton beams. This will contribute to optimizing the operation of high-power proton accelerators by minimizing beam loss, activation, and damage to both the diagnostics and the accelerator components.
Fermilab aims to provide greater beam power for the neutrino physics program. As the beam power increases, the unwanted production of secondary electrons in the beam pipe, known as ‘electron cloud’ or ‘E-cloud’ may become disruptive to high intensity operation. Instrumentation has been deployed in the Fermilab Main Injector (MI) to study E-cloud. One of these is a Retard Field Analyzer (RFA) that can be used to directly measure E-cloud generation at the location of the instrument. Studies of the dependence of E-cloud on beam intensity and bunch length have been carried out. The experimental results are compared to POSINST simulations. These simulations are guided by measurements from a Secondary Electron Yield (SEY) test stand installed in the MI to measure the SEY of materials such as the beam pipe stainless steel. The SEY has a strong influence on the E-cloud density. Results of these comprehensive studies comparing the RFA data with realistic MI simulations will be presented.