Accurate prediction of nucleic binding residues is essential for the understanding of transcription and translation processes. Integration of feature- and template-based strategies could improve the ...prediction of these key residues in proteins. Nevertheless, traditional hybrid algorithms have been surpassed by recently developed deep learning-based methods, and the possibility of integrating deep learning- and template-based approaches to improve performance remains to be explored. To address these issues, we developed a novel structure-based integrative algorithm called NABind that can accurately predict DNA- and RNA-binding residues. A deep learning module was built based on the diversified sequence and structural descriptors and edge aggregated graph attention networks, while a template module was constructed by transforming the alignments between the query and its multiple templates into features for supervised learning. Furthermore, the stacking strategy was adopted to integrate the above two modules for improving prediction performance. Finally, a post-processing module dependent on the random walk algorithm was proposed to further correct the integrative predictions. Extensive evaluations indicated that our approach could not only achieve excellent performance on both native and predicted structures but also outperformed existing hybrid algorithms and recent deep learning methods. The NABind server is available at
http://liulab.hzau.edu.cn/NABind/
.
Single-epoch virial black hole (BH) mass estimators utilizing broad emission lines have been routinely applied to high-redshift quasars to estimate their BH masses. Depending on the redshift, ...different line estimators (H alpha , H beta , Mg II lambda2798, C IV lambda1549) are often used with optical/near-infrared spectroscopy. Here, we use a homogeneous sample of 60 intermediate-redshift (z ~ 1.5-2.2) Sloan Digital Sky Survey quasars with optical and near-infrared spectra covering C IV through H alpha to investigate the consistency between different single-epoch virial BH mass estimators. We discuss controversial claims in the literature on the correlation between C iv and H beta FWHMs, and suggest that the reported correlation is either a result based on small samples or only valid for low-luminosity objects.
We present a simple framework for the growth and evolution of supermassive black holes (SMBHs) in the hierarchical structure formation paradigm, adopting the general idea that quasar activity is ...triggered in major mergers. In our model, black hole accretion is triggered during major mergers (mass ratio 0.3) of host dark matter halos. The successive evolution of quasar luminosities follows a universal light-curve (LC) form during which the growth of the SMBH is modeled self-consistently: an initial exponential growth at a constant Eddington ratio of order unity until it reaches the peak luminosity, followed by a power-law decay. Assuming that the peak luminosity correlates with the post-merger halo mass, we convolve the LC with the triggering rate of quasar activity to predict the quasar luminosity function (LF). Our model reproduces the observed LF at 0.5 < z < 4.5 for the full luminosity ranges probed by current optical and X-ray surveys. At z < 0.5, our model underestimates the LF at L bol < 1045 erg s-1, allowing room for the active galactic nuclei (AGNs) activity triggered by secular processes instead of major mergers. At z > 4.5, in order to reproduce the observed quasar abundance, the typical quasar hosts must shift to lower mass halos, and/or minor mergers can also trigger quasar activity. Our model reproduces both the observed redshift evolution and luminosity dependence of the linear bias of quasar/AGN clustering. Due to the scatter between instantaneous luminosity and halo mass, quasar/AGN clustering weakly depends on luminosity at low-to-intermediate luminosities; but the linear bias rises rapidly with luminosity at the high luminosity end and at high redshift. In our model, the Eddington ratio distribution is roughly lognormal, which broadens and shifts to lower mean values from high luminosity quasars (L bol 1046 erg s-1) to low-luminosity AGNs (L bol 1045 erg s-1), in good agreement with observations. The model predicts that the vast majority of 108.5 M SMBHs were already in place by z = 1, and 50% of them were in place by z = 2; but the less massive (107 M ) SMBHs were assembled more recently, likely more through secular processes than by major mergers-in accordance with the downsizing picture of SMBH assembly since the peak of bright quasar activity around z ~ 2-3.
Quasars are rapidly accreting supermassive black holes at the centres of massive galaxies. They display a broad range of properties across all wavelengths, reflecting the diversity in the physical ...conditions of the regions close to the central engine. These properties, however, are not random, but form well-defined trends. The dominant trend is known as 'Eigenvector 1', in which many properties correlate with the strength of optical iron and O III emission. The main physical driver of Eigenvector 1 has long been suspected to be the quasar luminosity normalized by the mass of the hole (the 'Eddington ratio'), which is an important parameter of the black hole accretion process. But a definitive proof has been missing. Here we report an analysis of archival data that reveals that the Eddington ratio indeed drives Eigenvector 1. We also find that orientation plays a significant role in determining the observed kinematics of the gas in the broad-line region, implying a flattened, disk-like geometry for the fast-moving clouds close to the black hole. Our results show that most of the diversity of quasar phenomenology can be unified using two simple quantities: Eddington ratio and orientation.
Nonlinear oscillators arise everywhere in engineering, and though there are many analytical methods available, a fast and accurate estimation of the frequency–amplitude relationship is much needed in ...practical applications. He’s frequency formulation meets this requirement, but the local points are chosen randomly. In this paper, the Gaussian interpolation points are adopted, making He’s method more mathematically rigorous and physically reliable. The cubic-quintic Duffing equation is used for comparison, and an excellent result is obtained.
We compute perturbative corrections to B→π form factors from QCD light-cone sum rules with B-meson distribution amplitudes. Applying the method of regions we demonstrate factorization of the ...vacuum-to-B-meson correlation function defined with an interpolating current for pion, at one-loop level, explicitly in the heavy quark limit. The short-distance functions in the factorization formulae of the correlation function involves both hard and hard-collinear scales; and these functions can be further factorized into hard coefficients by integrating out the hard fluctuations and jet functions encoding the hard-collinear information. Resummation of large logarithms in the short-distance functions is then achieved via the standard renormalization-group approach. We further show that structures of the factorization formulae for fBπ+(q2) and fBπ0(q2) at large hadronic recoil from QCD light-cone sum rules match that derived in QCD factorization. In particular, we perform an exploratory phenomenological analysis of B→π form factors, paying attention to various sources of perturbative and systematic uncertainties, and extract |Vub|=(3.05−0.38+0.54|th.±0.09|exp.)×10−3 with the inverse moment of the B-meson distribution amplitude ϕB+(ω) determined by reproducing fBπ+(q2=0) obtained from the light-cone sum rules with π distribution amplitudes. Furthermore, we present the invariant-mass distributions of the lepton pair for B→πℓνℓ (ℓ=μ,τ) in the whole kinematic region. Finally, we discuss non-valence Fock state contributions to the B→π form factors fBπ+(q2) and fBπ0(q2) in brief.
Combined organic and inorganic fouling is a primary barrier constraining the performance of reverse osmosis (RO) membrane. In this work, we conducted a systematic study focusing on the synergetic ...fouling effects of silica and humic acid (HA) in RO process, and found the critical silica concentration where the fouling pattern changed qualitatively. When the silica concentration was lower than 6 mM at a typical HA concentration of 50 mg·L−1, no severe fouling was observed, while silica reaching this critical point could cause severe synergetic fouling with HA. Concentrated silica above the critical point acted as the prior foulant with marginal fouling effect caused by HA. A variety of solutions and surface-based characterizations were performed to elucidate the synergistic fouling responsibility for silica and HA. Our study suggests that the carboxylic groups from HA formed hydrogen bonds with silica hydrate, inducing silica adsorption onto HA aggregates at low silica particle concentrations. The HA network was bridged together to form large foulants due to the silica-silica interaction above the silica critical concentration. These mechanisms were further confirmed by molecular dynamics simulations. This study provides an in-depth insight into the combined organic-inorganic fouling and can serve as a guideline to optimize feed conditions in order to mitigate fouling of RO in wastewater reusing industry.
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Abstract
We present a catalog of 1.4 million photometrically selected quasar candidates in the southern hemisphere over the ∼5000 deg
2
Dark Energy Survey (DES) wide survey area. We combine optical ...photometry from the DES second data release (DR2) with available near-infrared (NIR) and the all-sky unWISE mid-infrared photometry in the selection. We build models of quasars, galaxies, and stars with multivariate skew-
t
distributions in the multidimensional space of relative fluxes as functions of redshift (or color for stars) and magnitude. Our selection algorithm assigns probabilities for quasars, galaxies, and stars and simultaneously calculates photometric redshifts (photo-
z
) for quasar and galaxy candidates. Benchmarking on spectroscopically confirmed objects, we successfully classify (with photometry) 94.7% of quasars, 99.3% of galaxies, and 96.3% of stars when all IR bands (NIR
YJHK
and WISE W1W2) are available. The classification and photo-
z
regression success rates decrease when fewer bands are available. Our quasar (galaxy) photo-
z
quality, defined as the fraction of objects with the difference between the photo-
z z
p
and the spectroscopic redshift
z
s
, ∣Δ
z
∣ ≡ ∣
z
s
−
z
p
∣/(1 +
z
s
) ≤ 0.1, is 92.2% (98.1%) when all IR bands are available, decreasing to 72.2% (90.0%) using optical DES data only. Our photometric quasar catalog achieves an estimated completeness of 89% and purity of 79% at
r
< 21.5 (0.68 million quasar candidates), with reduced completeness and purity at 21.5 <
r
≲ 24. Among the 1.4 million quasar candidates, 87,857 have existing spectra, and 84,978 (96.7%) of them are spectroscopically confirmed quasars. Finally, we provide quasar, galaxy, and star probabilities for all (0.69 billion) photometric sources in the DES DR2 coadded photometric catalog.
We jointly constrain the luminosity function (LF) and black hole mass function (BHMF) of broad-line quasars with forward Bayesian modeling in the quasar mass-luminosity plane, based on a homogeneous ...sample of ~58, 000 Sloan Digital Sky Survey (SDSS) Data Release 7 quasars at z ~ 0.3-5. We take into account the selection effect of the sample flux limit; more importantly, we deal with the statistical scatter between true BH masses and FWHM-based single-epoch virial mass estimates, as well as potential luminosity-dependent biases of these mass estimates. The LF is tightly constrained in the regime sampled by SDSS and makes reasonable predictions when extrapolated to ~3 mag fainter. Downsizing is seen in the model LF. On the other hand, we find it difficult to constrain the BHMF to within a factor of a few at z > ~0.7 (with Mg II and C IV-based virial BH masses). This is mainly driven by the unknown luminosity-dependent bias of these mass estimators and its degeneracy with other model parameters, and secondly driven by the fact that SDSS quasars only sample the tip of the active BH population at high redshift. Nevertheless, the most likely models favor a positive luminosity-dependent bias for Mg II and possibly for C IV, such that at fixed true BH mass, objects with higher-than-average luminosities have overestimated FWHM-based virial masses. There is tentative evidence that downsizing also manifests itself in the active BHMF, and the BH mass density in broad-line quasars contributes an insignificant amount to the total BH mass density at all times. Within our model uncertainties, we do not find a strong BH mass dependence of the mean Eddington ratio, but there is evidence that the mean Eddington ratio (at fixed BH mass) increases with redshift.
Artificial water channels are synthetic molecules that aim to mimic the structural and functional features of biological water channels (aquaporins). Here we report on a cluster-forming organic ...nanoarchitecture, peptide-appended hybrid4arene (PAH4), as a new class of artificial water channels. Fluorescence experiments and simulations demonstrated that PAH4s can form, through lateral diffusion, clusters in lipid membranes that provide synergistic membrane-spanning paths for a rapid and selective water permeation through water-wire networks. Quantitative transport studies revealed that PAH4s can transport >10
water molecules per second per molecule, which is comparable to aquaporin water channels. The performance of these channels exceeds the upper bound limit of current desalination membranes by a factor of ~10
, as illustrated by the water/NaCl permeability-selectivity trade-off curve. PAH4's unique properties of a high water/solute permselectivity via cooperative water-wire formation could usher in an alternative design paradigm for permeable membrane materials in separations, energy production and barrier applications.
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