Free-energy calculations have seen increased usage in structure-based drug design. Despite the rising interest, automation of the complex calculations and subsequent analysis of their results are ...still hampered by the restricted choice of available tools. In this work, an application for automated setup and processing of free-energy calculations is presented. Several sanity checks for assessing the reliability of the calculations were implemented, constituting a distinct advantage over existing open-source tools. The underlying workflow is built on top of the software Sire, SOMD, BioSimSpace, and OpenMM and uses the AMBER 14SB and GAFF2.1 force fields. It was validated on two datasets originally composed by Schrödinger, consisting of 14 protein structures and 220 ligands. Predicted binding affinities were in good agreement with experimental values. For the larger dataset, the average correlation coefficient
was 0.70 ± 0.05 and average Kendall's τ was 0.53 ± 0.05, which are broadly comparable to or better than previously reported results using other methods.
We present the ATLAS discovery and initial analysis of the first 18 days of the unusual transient event, ATLAS18qqn/AT2018cow. It is characterized by a high peak luminosity (∼1.7 × 1044 erg s−1), ...rapidly evolving light curves (>5 mag rise to peak in ∼3.5 days), and hot blackbody spectra, peaking at ∼27,000 K that are relatively featureless and unchanging over the first two weeks. The bolometric light curve cannot be powered by radioactive decay under realistic assumptions. The detection of high-energy emission may suggest a central engine as the powering source. Using a magnetar model, we estimated an ejected mass of 0.1-0.4 M , which lies between that of low-energy core-collapse events and the kilonova, AT2017gfo. The spectra cooled rapidly from 27,000 to 15,000 K in just over two weeks but remained smooth and featureless. Broad and shallow emission lines appear after about 20 days, and we tentatively identify them as He i although they would be redshifted from their rest wavelengths. We rule out that there are any features in the spectra due to intermediate mass elements up to and including the Fe group. The presence of r-process elements cannot be ruled out. If these lines are due to He, then we suggest a low-mass star with residual He as a potential progenitor. Alternatively, models of magnetars formed in neutron star mergers, or accretion onto a central compact object, give plausible matches to the data.
We present a systematic investigation of muon-stopping states in superconductors that reportedly exhibit spontaneous magnetic fields below their transition temperatures due to time-reversal symmetry ...breaking. These materials include elemental rhenium, several intermetallic systems, and Sr_{2}RuO_{4}. We demonstrate that the presence of the muon leads to only a limited and relatively localized perturbation to the local crystal structure, while any small changes to the electronic structure occur several electron volts below the Fermi energy, leading to only minimal changes in the charge density on ions close to the muon. Our results imply that the muon-induced perturbation alone is unlikely to lead to the observed spontaneous fields in these materials, whose origin is more likely intrinsic to the time-reversal symmetry-broken superconducting state.
Key insights into the behavior of materials can be gained by observing their structure as they undergo lattice distortion. Laser pulses on the femtosecond time scale can be used to induce disorder in ...a "pump-probe" experiment with the ensuing transients being probed stroboscopically with femtosecond pulses of visible light, x-rays, or electrons. Here we report three-dimensional imaging of the generation and subsequent evolution of coherent acoustic phonons on the picosecond time scale within a single gold nanocrystal by means of an x-ray free-electron laser, providing insights into the physics of this phenomenon. Our results allow comparison and confirmation of predictive models based on continuum elasticity theory and molecular dynamics simulations.
The Asteroid Terrestrial impact Last Alert System (ATLAS) system consists of two 0.5 m Schmidt telescopes with cameras covering 29 square degrees at plate scale of 1.86 arcsec per pixel. Working in ...tandem, the telescopes routinely survey the whole sky visible from Hawaii (above δ > − 50 ° ) every two nights, exposing four times per night, typically reaching o < 19 magnitude per exposure when the moon is illuminated and c < 19.5 magnitude per exposure in dark skies. Construction is underway of two further units to be sited in Chile and South Africa which will result in an all-sky daily cadence from 2021. Initially designed for detecting potentially hazardous near earth objects, the ATLAS data enable a range of astrophysical time domain science. To extract transients from the data stream requires a computing system to process the data, assimilate detections in time and space and associate them with known astrophysical sources. Here we describe the hardware and software infrastructure to produce a stream of clean, real, astrophysical transients in real time. This involves machine learning and boosted decision tree algorithms to identify extragalactic and Galactic transients. Typically we detect 10-15 supernova candidates per night which we immediately announce publicly. The ATLAS discoveries not only enable rapid follow-up of interesting sources but will provide complete statistical samples within the local volume of 100 Mpc. A simple comparison of the detected supernova rate within 100 Mpc, with no corrections for completeness, is already significantly higher (factor 1.5 to 2) than the current accepted rates.
The energy landscape of carbon is exceedingly complex, hosting diverse and important metastable phases, including diamond, fullerenes, nanotubes, and graphene. Searching for structures, especially ...those with large unit cells, in this landscape is challenging. Here we use a combined stochastic search strategy employing two algorithms (ab initio random structure search and random sampling strategy combined with space group and graph theory) to apply connectivity constraints to unit cells containing up to 100 carbon atoms. We uncover three low energy carbon polymorphs (Pbam-32, P6/mmm, and I4over ¯3d) with new topologies, containing 32, 36, and 94 atoms in their primitive cells, respectively. Their energies relative to diamond are 96, 131, and 112 meV/atom, respectively, which suggests potential metastability. These three carbon allotropes are mechanically and dynamically stable, insulating carbon crystals with superhard mechanical properties. The I4over ¯3d structure possesses a direct band gap of 7.25 eV, which is the widest gap in the carbon allotrope family. Silicon, germanium, and tin versions of Pbam-32, P6/mmm, and I4over ¯3d also show energetic, dynamical, and mechanical stability. The computed electronic properties show that they are potential materials for semiconductor and photovoltaic applications.
The VLT-FLAMES Tarantula Survey Sana, H; de Koter, A; de Mink, S E ...
Astronomy and astrophysics (Berlin),
02/2013, Letnik:
550
Journal Article
Recenzirano
Odprti dostop
The Tarantula Nebula in the Large Magellanic Cloud is our closest view of a starburst region and is the ideal environment to investigate important questions regarding the formation, evolution and ...final fate of the most massive stars. We analyze the multiplicity properties of the massive O-type star population observed through multi-epoch spectroscopy in the framework of the VLT-FLAMES Tarantula Survey. With 360 O-type stars, this is the largest homogeneous sample of massive stars analyzed to date. Using the multiplicity properties of the O stars in the Tarantula region and simple evolutionary considerations, we estimate that over 50% of the current O star population will exchange mass with its companion within a binary system. This shows that binary interaction is greatly affecting the evolution and fate of massive stars, and must be taken into account to correctly interpret unresolved populations of massive stars.
The Wet Chemistry Laboratory on the Phoenix Mars Lander performed aqueous chemical analyses of martian soil from the polygon-patterned northern plains of the Vastitas Borealis. The solutions ...contained approximately 10 mM of dissolved salts with 0.4 to 0.6% perchlorate (ClO₄) by mass leached from each sample. The remaining anions included small concentrations of chloride, bicarbonate, and possibly sulfate. Cations were dominated by Mg²⁺ and Na⁺, with small contributions from K⁺ and Ca²⁺. A moderately alkaline pH of 7.7 ± 0.5 was measured, consistent with a carbonate-buffered solution. Samples analyzed from the surface and the excavated boundary of the approximately 5-centimeter-deep ice table showed no significant difference in soluble chemistry.
Lymph node density (LND) has previously been reported to reliably predict recurrence risk and survival in oral cavity squamous cell carcinoma (OSCC). This multicenter international study was designed ...to validate the concept of LND in OSCC.
The study included 4254 patients diagnosed as having OSCC. The median follow-up was 41 months. Five-year overall survival (OS), disease-specific survival (DSS), disease-free survival (DFS), locoregional control and distant metastasis rates were calculated using the Kaplan-Meier method. Lymph node density (number of positive lymph nodes/total number of excised lymph nodes) was subjected to multivariate analysis.
The OS was 49% for patients with LND0.07 compared with 35% for patients with LND>0.07 (P<0.001). Similarly, the DSS was 60% for patients with LND0.07 compared with 41% for those with LND>0.07 (P<0.001). Lymph node density reliably stratified patients according to their risk of failure within the individual N subgroups (P=0.03). A modified TNM staging system based on LND ratio was consistently superior to the traditional system in estimating survival measures.
This multi-institutional study validates the reliability and applicability of LND as a predictor of outcomes in OSCC. Lymph node density can potentially assist in identifying patients with poor outcomes and therefore for whom more aggressive adjuvant treatment is needed.
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