To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

We study the "entanglement spectrum" (a presentation of the Schmidt decomposition analogous to a set of "energy levels") of a many-body state, and compare the Moore-Read model wave function for the nu=5/2 fractional quantum Hall state with a generic 5/2 state obtained by finite-size diagonalization of the second-Landau-level-projected Coulomb interactions. Their spectra share a common "gapless" structure, related to conformal field theory. In the model state, these are the only levels, while in the "generic" case, they are separated from the rest of the spectrum by a clear "entanglement gap", which appears to remain finite in the thermodynamic limit. We propose that the low-lying entanglement spectrum can be used as a "fingerprint" to identify topological order.

A very fast empirical method is presented for structure-based protein pKa prediction and rationalization. The desolvation effects and intra-protein interactions, which cause variations in pKa values of protein ionizable groups, are empirically related to the positions and chemical nature of the groups proximate to the pKa sites. A computer program is written to automatically predict pKa values based on these empirical relationships within a couple of seconds. Unusual pKa values at buried active sites, which are among the most interesting protein pKa values, are predicted very well with the empirical method. A test on 233 carboxyl, 12 cysteine, 45 histidine, and 24 lysine pKa values in various proteins shows a root-mean-square deviation (RMSD) of 0.89 from experimental values. Removal of the 29 pKa values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pKa values.

Real-world observable physical and chemical characteristics are increasingly being calculated from the 3D structures of biomolecules. Methods for calculating pKa values, binding constants of ligands, and changes in protein stability are readily available, but often the limiting step in computational biology is the conversion of PDB structures into formats ready for use with biomolecular simulation software. The continued sophistication and integration of biomolecular simulation methods for systems- and genome-wide studies requires a fast, robust, physically realistic and standardized protocol for preparing macromolecular structures for biophysical algorithms. As described previously, the PDB2PQR web server addresses this need for electrostatic field calculations (Dolinsky et al., Nucleic Acids Research, 32, W665–W667, 2004). Here we report the significantly expanded PDB2PQR that includes the following features: robust standalone command line support, improved pKa estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code. These features are available through a new web interface (http://pdb2pqr.sourceforge.net/), which offers users a wide range of options for PDB file conversion, modification and parameterization.

The relationships among the macroscopic compositional parameters of a Cu-exchanged SSZ-13 zeolite catalyst, the types and numbers of Cu active sites, and activity for the selective catalytic reduction (SCR) of NOx with NH3 are established through experimental interrogation and computational analysis of materials across the catalyst composition space. Density functional theory, stochastic models, and experimental characterizations demonstrate that within the synthesis protocols applied here and across Si:Al ratios, the volumetric density of six-membered-rings (6MR) containing two Al (2Al sites) is consistent with a random Al siting in the SSZ-13 lattice subject to Löwenstein's rule. Further, exchanged Cu(II) ions first populate these 2Al sites before populating remaining unpaired, or 1Al, sites as Cu(II)OH. These sites are distinguished and enumerated ex situ through vibrational and X-ray absorption spectroscopies (XAS) and chemical titrations. In situ and operando XAS follow Cu oxidation state and coordination environment as a function of environmental conditions including low-temperature (473 K) SCR catalysis and are rationalized through first-principles thermodynamics and ab initio molecular dynamics. Experiment and theory together reveal that the Cu sites respond sensitively to exposure conditions, and in particular that Cu species are solvated and mobilized by NH3 under SCR conditions. While Cu sites are spectroscopically and chemically distinct away from these conditions, they exhibit similar turnover rates, apparent activation energies and apparent reaction orders at the SCR conditions, even on zeolite frameworks other than SSZ13.

Copper ions exchanged into zeolites are active for the selective catalytic reduction (SCR) of nitrogen oxides (NO ) with ammonia (NH), but the low-temperature rate dependence on copper (Cu) volumetric density is inconsistent with reaction at single sites. We combine steady-state and transient kinetic measurements, x-ray absorption spectroscopy, and first-principles calculations to demonstrate that under reaction conditions, mobilized Cu ions can travel through zeolite windows and form transient ion pairs that participate in an oxygen (O)-mediated Cu→Cu redox step integral to SCR. Electrostatic tethering to framework aluminum centers limits the volume that each ion can explore and thus its capacity to form an ion pair. The dynamic, reversible formation of multinuclear sites from mobilized single atoms represents a distinct phenomenon that falls outside the conventional boundaries of a heterogeneous or homogeneous catalyst.

Elaborate design of highly active and stable catalysts from Earth-abundant elements has great potential to produce materials that can replace the noble-metal-based catalysts commonly used in a range of useful (electro)chemical processes. Here we report, for the first time, a synthetic method that leads to in situ growth of {2̅10} high-index faceted Ni3S2 nanosheet arrays on nickel foam (NF). We show that the resulting material, denoted Ni3S2/NF, can serve as a highly active, binder-free, bifunctional electrocatalyst for both the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER). Ni3S2/NF is found to give ∼100% Faradaic yield toward both HER and OER and to show remarkable catalytic stability (for >200 h). Experimental results and theoretical calculations indicate that Ni3S2/NF's excellent catalytic activity is mainly due to the synergistic catalytic effects produced in it by its nanosheet arrays and exposed {2̅10} high-index facets.

While mutations affecting protein-coding regions have been examined across many cancers, structural variants at the genome-wide level are still poorly defined. Through integrative deep whole-genome and -transcriptome analysis of 101 castration-resistant prostate cancer metastases (109X tumor/38X normal coverage), we identified structural variants altering critical regulators of tumorigenesis and progression not detectable by exome approaches. Notably, we observed amplification of an intergenic enhancer region 624 kb upstream of the androgen receptor (AR) in 81% of patients, correlating with increased AR expression. Tandem duplication hotspots also occur near MYC, in lncRNAs associated with post-translational MYC regulation. Classes of structural variations were linked to distinct DNA repair deficiencies, suggesting their etiology, including associations of CDK12 mutation with tandem duplications, TP53 inactivation with inverted rearrangements and chromothripsis, and BRCA2 inactivation with deletions. Together, these observations provide a comprehensive view of how structural variations affect critical regulators in metastatic prostate cancer.