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We investigate the electronic structure and lattice stability of pristine and functionalized (with either hydrogen or oxygen) $\alpha$-graphyne systems. We identify lattice instabilities due to soft-phonon modes, and describe two mechanisms leading to gap opening in the Dirac-fermion electronic spectrum of these systems: symmetry breaking, connected with the lattice instabilities, and partial incorporation of an $sp^3$-hybrid character in the covalent-bonding network of a buckled hydrogenated $\alpha$-graphyne lattice that retains the symmetries of the parent pristine $\alpha$-graphyne. In the case of an oxygen-functionalized $\alpha$-graphyne structure, each O atom binds asymmetrically to two twofold-coordinated C atoms, breaking inversion and mirror symmetries, and leading to the opening of a sizeable gap of 0.22 eV at the Dirac point. Generally, mirror symmetries are found to suffice for the occurrence of gapless Dirac cones in these $\alpha$-graphyne systems, even in the absence of inversion symmetry centers. Moreover, we analyze the gapless and gapped Dirac cones of pristine and functionalized $\alpha$-graphynes from the perspective of the dispersion relations for massless and massive free Dirac fermions. We find that mirror-symmetry breaking mimics a Dirac-fermion mass-generation mechanism in the oxygen-functionalized $\alpha$-graphyne, leading to gap opening and to isotropic electronic dispersions with a rather small electron-hole asymmetry. In the hydrogen-functionalized case, we find that carriers show a remarkable anisotropy, behaving as massless fermions along the M-K line in the Brillouin zone and as massive fermions along the $\Gamma$-K line., Comment: 9 pages in two column format, 7 figures and 2 tables Submitted for publication in Chemistry of Materials

The isothermal compressibility of water is essential to understand its anomalous properties. We compute it by ab initio molecular dynamics simulations of 200 molecules at five densities, using two different van der Waals density functionals. While both functionals predict compressibilities within ~30% of experiment, only one of them accurately reproduces, within the uncertainty of the simulation, the density dependence of the self-diffusion coefficient in the anomalous region. The discrepancies between the two functionals are explained in terms of the low- and high-density structures of the liquid., Comment: 12 pages, 16 figures

We perform ab initio calculations that indicate that the relative stability of antiphase boundaries (APB) with armchair and zigzag chiralities in monolayer boron nitride (BN) is determined by the chemical potentials of the boron and nitrogen species in the synthesis process. In an N-rich environment, a zigzag APB with N-rich core is the most stable structure, while under B-rich or intrinsic growth conditions, an armchair APB with stoichiometric core is the most stable. This stability transition is shown to arise from a competition between homopolar-bond (B-B and N-N) and elastic energy costs in the core of the APBs. Moreover, in the presence of a carbon source we find that a carbon-doped zigzag APB becomes the most stable boundary near the N-rich limit. The electronic structure of the two types of APBs in BN is shown to be particularly distinct, with the zigzag APB depicting defect-like deep electronic bands in the band gap, while the armchair APB shows bulk-like shallow electronic bands., Comment: 22 pages on reprint format; 8 figures

The authors measure the persistence and contour lengths of DNA-psoralen complexes, as a function of psoralen concentration, for intercalated and crosslinked complexes. In both cases, the persistence length monotonically increases until a certain critical concentration is reached, above which it abruptly decreases and remains approximately constant. The contour length of the complexes exhibits no such discontinuous behavior. By fitting the relative increase of the contour length to the neighbor exclusion model, we obtain the exclusion number and the intrinsic intercalating constant of the psoralen-DNA interaction. Ab initio calculations are employed in order to provide an atomistic picture of these experimental findings., Comment: 9 pages, 4 figures in re-print format 3 pages, 4 figures in the published version