Redesigning Vina@QNLM for Ultra-Large-Scale Molecular Docking and Screening on a Sunway Supercomputer

Ultra-large-scale molecular docking can improve the accuracy of lead compounds in drug discovery. In this study, we developed a molecular docking piece of software, Vina@QNLM, which can use more than 4,80,000 parallel processes to search for potential lead compounds from hundreds of millions of compounds. We proposed a task scheduling mechanism for large-scale parallelism based on Vinardo and Sunway supercomputer architecture. Then, we readopted the core docking algorithm to incorporate the full advantage of the heterogeneous multicore processor architecture in intensive computing. We successfully expanded it to 10, 465, 065 cores (1,61,001 management process elements and 0, 465, 065 computing process elements), with a strong scalability of 55.92%. To the best of our knowledge, this is the first time that 10 million cores are used for molecular docking on Sunway. The introduction of the heterogeneous multicore processor architecture achieved the best speedup, which is 11x more than that of the management process element of Sunway. The performance of Vina@QNLM was comprehensively evaluated using the CASF-2013 and CASF-2016 protein–ligand benchmarks, and the screening power was the highest out of the 27 pieces of software tested in the CASF-2013 benchmark. In some existing applications, we used Vina@QNLM to dock more than 10 million molecules to nine rigid proteins related to SARS-CoV-2 within 8.5 h on 10 million cores. We also developed a platform for the general public to use the software.

Low Temperature Sealing Process and Properties of Kovar Alloy to DM305 Electronic Glass

The low temperature sealing of Kovar alloy to DM305 electronic glass was realized by using lead-free glass solder of the Bi2O3-ZnO-B2O3 system in atmospheric environment. The sealing process was optimized by pre-oxidation of Kovar alloy and low temperature founding of flake glass solder. The effects of sealing temperature and holding time on the properties of sealing joint were studied by means of X-ray diffraction (XRD), scanning electron microscope (SEM), energy dispersive X-ray spectroscopy (EDS), etc. The results showed that the pre-oxidized Kovar alloy and DM305 electronic glass were successfully sealed with flake glass solder at the sealing temperature of 500 °C for 20 min. Meanwhile, the joint interface had no pores, cracks, and other defects, the shear strength was 12.24 MPa, and the leakage rate of air tightness was 8 × 10−9 Pa·m3/s. During the sealing process, element Bi in glass solder diffused into the oxide layer of Kovar alloy and DM305 electronic glass about 1 μm, respectively.

SALT revisits DY Cen: a rapidly evolving strontium-rich single helium star

ABSTRACT The hydrogen-deficient star DY Cen has been reported as an R CrB-type variable, an extreme helium star (with some hydrogen), and as a single-lined spectroscopic binary. It has been associated with a dramatic change in visual brightness and colour corresponding to a change in effective temperature ( Teff) of some 20 000 K in the last century. To characterize the binary orbit and Teff changes more precisely, new high-resolution spectroscopy has been obtained with SALT. The previous orbital period is not confirmed; previous measurements may have been confused by the presence of pulsations. Including data from earlier epochs (1987, 2002, and 2010), self-consistent spectral analyses from all four epochs demonstrate an increase in Teff from 18 800 to 24 400 K between 1987 and 2015. Line profiles demonstrate that the surface rotation has increased by a factor of 2 over the same interval. This is commensurate with the change in Teff and an overall contraction. Rotation will exceed critical if contraction continues. The 1987 spectrum shows evidence of a very high abundance of the s-process element strontium. The very rapid evolution, non-negligible surface hydrogen and high surface strontium point to a history involving a very late thermal pulse. Observations over the next 30 yr should look for a decreasing pulsation period, reactivation of R CrB-type activity as the star seeks to shed angular momentum and increasing illumination by emission lines from nebular material ejected in the past.

The GALAH survey: temporal chemical enrichment of the galactic disc

ABSTRACT We present isochrone ages and initial bulk metallicities ($\rm [Fe/H]_{bulk}$, by accounting for diffusion) of 163 722 stars from the GALAH Data Release 2, mainly composed of main-sequence turn-off stars and subgiants ($7000\, \mathrm{ K}> T_{\mathrm{ eff}}> 4000\, \mathrm{ K}$ and $\log g>3$ dex). The local age–metallicity relationship (AMR) is nearly flat but with significant scatter at all ages; the scatter is even higher when considering the observed surface abundances. After correcting for selection effects, the AMR appears to have intrinsic structures indicative of two star formation events, which we speculate are connected to the thin and thick discs in the solar neighbourhood. We also present abundance ratio trends for 16 elements as a function of age, across different $\rm [Fe/H]_{bulk}$ bins. In general, we find the trends in terms of [X/Fe] versus age from our far larger sample to be compatible with studies based on small (∼100 stars) samples of solar twins, but we now extend them to both sub- and supersolar metallicities. The α-elements show differing behaviour: the hydrostatic α-elements O and Mg show a steady decline with time for all metallicities, while the explosive α-elements Si, Ca, and Ti are nearly constant during the thin-disc epoch (ages $\lesssim \! 12$ Gyr). The s-process elements Y and Ba show increasing [X/Fe] with time while the r-process element Eu has the opposite trend, thus favouring a primary production from sources with a short time delay such as core-collapse supernovae over long-delay events such as neutron star mergers.

Neutron-capture elements in dwarf galaxies

The heavy elements (Z > 30) are created in neutron (n)-capture processes that are predicted to happen at vastly different nucleosynthetic sites. To study these processes in an environment different from the Milky Way, we targeted the n-capture elements in red giant branch stars in the Sculptor dwarf spheroidal galaxy. Using ESO VLT/FLAMES spectra, we measured the chemical abundances of Y, Ba, La, Nd, and Eu in 98 stars covering the metalliticy range −2.4 < [Fe/H] < −0.9. This is the first paper in a series about the n-capture elements in dwarf galaxies, and here we focus on the relative and absolute timescales of the slow (s)- and rapid (r)-processes in Sculptor. From the abundances of the s-process element Ba and the r-process element Eu, it is clear that the r-process enrichment occurred throughout the entire chemical evolution history of Sculptor. Furthermore, there is no evidence for the r-process to be significantly delayed in time relative to core-collapse supernovae. Neutron star mergers are therefore unlikely the dominant (or only) nucleosynthetic site of the r-process. However, the products of the s-process only become apparent at [Fe/H] ≈ −2 in Sculptor, and the s-process becomes the dominant source of Ba at [Fe/H] ≳ −2. We tested the use of [Y/Mg] and [Ba/Mg] as chemical clocks in Sculptor. Similarly to what is observed in the Milky Way, [Y/Mg] and [Ba/Mg] increase towards younger ages. However, there is an offset in the trends, where the abundance ratios of [Y/Mg] in Sculptor are significantly lower than those of the Milky Way at any given age. This is most likely caused by metallicity dependence of yields from the s-process, as well as by a different relative contribution of the s-process to core-collapse supernovae in these galaxies. Comparisons of our results with data of the Milky Way and the Fornax dwarf spheroidal galaxy furthermore show that these chemical clocks depend on both metallicity and environment.

H-band discovery of additional second-generation stars in the Galactic bulge globular cluster NGC 6522 as observed by APOGEE and Gaia

We present an elemental abundance analysis of high-resolution spectra for five giant stars spatially located within the innermost regions of the bulge globular cluster NGC 6522 and derive Fe, Mg, Al, C, N, O, Si, and Ce abundances based on H-band spectra taken with the multi-object APOGEE-north spectrograph from the SDSS-IV Apache Point Observatory Galactic Evolution Experiment (APOGEE) survey. Of the five cluster candidates, two previously unremarked stars are confirmed to have second-generation (SG) abundance patterns, with the basic pattern of depletion in C and Mg simultaneous with enrichment in N and Al as seen in other SG globular cluster populations at similar metallicity. In agreement with the most recent optical studies, the NGC 6522 stars analyzed exhibit (when available) only mild overabundances of the s-process element Ce, contradicting the idea that NGC 6522 stars are formed from gas enriched by spinstars and indicating that other stellar sources such as massive AGB stars could be the primary polluters of intra-cluster medium. The peculiar abundance signatures of SG stars have been observed in our data, confirming the presence of multiple generations of stars in NGC 6522.

Breaking the dichotomy between typical and anomalous globular clusters: the case of NGC 3201

We recently discovered that NGC 3201 has characteristics that set it outside the current twofold classification scheme for Galactic globular clusters (GCs). Most GCs are mono-metallic and show light-element abundance variations (e.g., Na-O and C-N anti-correlations); but a minority of clusters also present variations in Fe correlating with s-process element and C+N+O abundances, and they possess multiple C-N sequences. These anomalous GCs also have a broad sub-giant branch (SGB) and follow the same mass-size relation as dwarf galaxies possibly evolving into GCs. We now revealed that NGC 3201 belongs to neither group. It has multiple C-N sequences, but no broad SGB, no strong evidence of a Fe-spread, and it does not follow the mass-size relation.

S stars and s-process in the Gaia era

Context. S stars are transition objects between M-type giants and carbon stars on the asymptotic giant branch (AGB). They are characterized by overabundances of s-process elements. Roughly half of them are enhanced in technetium (Tc), an s-process element with no stable isotope, while the other half lack technetium. This dichotomy arises from the fact that Tc-rich S stars are intrinsically producing s-process elements and have undergone third dredge-up (TDU) events, while Tc-poor S stars owe their s-process overabundances to a past pollution by a former AGB companion which is now an undetected white dwarf, and since the epoch of the mass transfer, technetium has totally decayed. Aims. Our aim is to analyse the abundances of S stars and gain insights into their evolutionary status and on the nucleosynthesis of heavy s-process elements taking place in their interior. In particular, the location of extrinsic and intrinsic S stars in the HR diagram will be compared with the theoretical onset of the TDU on the thermally pulsing AGB. Methods. A sample of 19 S-type stars was analysed by combining HERMES high-resolution spectra, accurate Gaia Data Release 2 (GDR2) parallaxes, stellar-evolution models, and newly designed MARCS model atmospheres for S-type stars. Various stellar parameters impact the atmospheric structure of S stars, not only effective temperature, gravity, metallicity and microturbulence but also C/O and [s/Fe]. We show that photometric data alone are not sufficient to disentangle these parameters. We present a new automatic spectral-fitting method that allows one to constrain the range of possible atmospheric parameters. Results. Combining the derived parameters with GDR2 parallaxes allows a joint analysis of the location of the stars in the Hertzsprung–Russell diagram and of their surface abundances. For all 19 stars, Zr and Nb abundances are derived, complemented by abundances of other s-process elements for the three Tc-rich S stars. These abundances agree within the uncertainties with nucleosynthesis predictions for stars of corresponding mass, metallicity and evolutionary stage. The Tc dichotomy between extrinsic and intrinsic S stars is seen as well in the Nb abundances: intrinsic, Tc-rich S stars are Nb-poor, whereas extrinsic, Tc-poor S stars are Nb-rich. Most extrinsic S stars lie close to the tip of the red giant branch (RGB), and a few are located along the early AGB. All appear to be the cooler analogues of barium stars. Barium stars with masses smaller than 2.5 M⊙ turn into extrinsic S stars on the RGB, because only for those masses does the RGB tip extend to temperatures lower than ~4200 K, which allows the ZrO bands distinctive of S-type stars to develop. On the contrary, barium stars with masses in excess of ~2.5 M⊙ can only turn into extrinsic S stars on the E-AGB, but those are short-lived, and thus rare. The location of intrinsic S stars in the HR diagram is compatible with them being thermally-pulsing AGB stars. Although nucleosynthetic model predictions give a satisfactory distribution of s-process elements, fitting at the same time the carbon and heavy s-element enrichments still remains difficult. Finally, the Tc-rich star V915 Aql is challenging as it points at the occurrence of TDU episodes in stars with masses as low as M ~ 1 M⊙.