Electrostatic considerations affecting the calculated HOMO-LUMO gap in protein molecules.

A detailed study of energy differences between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO gaps) in protein systems and water clusters is presented. Recent work questioning the applicability of Kohn-Sham density-functional theory to proteins and large water clusters (E. Rudberg, J. Phys.: Condens. Mat. 2012, 24, 072202) has demonstrated vanishing HOMO-LUMO gaps for these systems, which is generally attributed to the treatment of exchange in the functional used. The present work shows that the vanishing gap is, in fact, an electrostatic artefact of the method used to prepare the system. Practical solutions for ensuring the gap is maintained when the system size is increased are demonstrated. This work has important implications for the use of large-scale density-functional theory in biomolecular systems, particularly in the simulation of photoemission, optical absorption and electronic transport, all of which depend critically on differences between energies of molecular orbitals.Comment: 13 pages, 4 figure

Localization and chiral symmetry in 2+1 flavor domain wall QCD

We present results for the dependence of the residual mass of domain wall fermions (DWF) on the size of the fifth dimension and its relation to the density and localization properties of low-lying eigenvectors of the corresponding hermitian Wilson Dirac operator relevant to simulations of 2+1 flavor domain wall QCD. Using the DBW2 and Iwasaki gauge actions, we generate ensembles of configurations with a $16^3\times 32$ space-time volume and an extent of 8 in the fifth dimension for the sea quarks. We demonstrate the existence of a regime where the degree of locality, the size of chiral symmetry breaking and the rate of topology change can be acceptable for inverse lattice spacings $a^{-1} \ge 1.6$ GeV.Comment: 59 Pages, 23 figures, 1 MPG linke

Studying the Physical Diversity of Late-M Dwarfs with Dynamical Masses

We present a systematic study of the physical properties of late-M dwarfs based on high-quality dynamical mass measurements and near-infrared (NIR) spectra. We use astrometry from Keck NGS and LGS AO imaging to determine orbits for late-M binaries. We find that LP 349-25 (M7.5+M8) is a pair of young brown dwarfs (Mtot = 0.120 Msun) for which Lyon and Tucson evolutionary models jointly predict an age of 140+/-30 Myr. This is consistent with the age of the Pleiades, but at least LP 349-25A defies the empirical Pleiades lithium depletion boundary, implying that the system is in fact older and that evolutionary models underpredict the component luminosities. We find that LHS 1901AB (M6.5+M6.5) is a pair of very low-mass stars (Mtot = 0.194 Msun) with model-derived ages consistent with limits from its lack of activity (> 6 Gyr). Our improved orbit for Gl 569Bab (M8.5+M9) results in a higher mass for this binary (Mtot = 0.140 Msun) compared to previous work (0.125 Msun). We use these masses along with our published results for 2MASS J2206-2047AB (M8+M8) to test four sets of ultracool model atmospheres currently in use. Fitting these models to our NIR integrated-light spectra provides temperature estimates warmer by ~250 K than those derived independently from Dusty evolutionary models given the measured masses and luminosities. We propose that model atmospheres are more likely to be the source of this discrepancy, as it would be difficult to explain a uniform temperature offset over such a wide range of masses, ages, and activity levels in the context of evolutionary models. Our results contrast those of Konopacky et al. as we find an opposite and smaller mass discrepancy from what they report when we adopt their model-testing approach since our Teff estimates from fitting spectra are ~650 K higher than from their fitting of broadband photometry alone.Comment: 53 pages, 12 figures, accepted to Ap

Galaxy formation in the Planck cosmology - III. The high-redshift universe

We present high-redshift predictions of the star formation rate distribution function (SFRDF), UV luminosity function (UVLF), galactic stellar mass function (GSMF), and specific star formation rates (sSFRs) of galaxies from the latest version of the Munich semi-analytic model L-GALAXIES. We find a good fit to both the shape and normalization of the SFRDF at z = 4–7, apart from a slight underprediction at the low-SFR end at z = 4. Likewise, we find a good fit to the faint number counts for the observed UVLF at brighter magnitudes our predictions lie below the observations, increasingly so at higher redshifts. At all redshifts and magnitudes, the raw (unattenuated) number counts for the UVLF lie above the observations. Because of the good agreement with the SFR we interpret our underprediction as an overestimate of the amount of dust in the model for the brightest galaxies, especially at high redshift. While the shape of our GSMF matches that of the observations, we lie between (conflicting) observations at z = 4–5, and underpredict at z = 6–7. The sSFRs of our model galaxies show the observed trend of increasing normalization with redshift, but do not reproduce the observed mass dependence. Overall, we conclude that the latest version of L-GALAXIES, which is tuned to match observations at z ≤ 3, does a fair job of reproducing the observed properties of galaxies at z ≥ 4. More work needs to be done on understanding observational bias at high redshift, and upon the dust model, before strong conclusions can be drawn on how to interpret remaining discrepancies between the model and observations

Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD

Background: The investigation of complex disease heterogeneity has been challenging. Here, we introduce a network-based approach, using partial correlations, that analyzes the relationships among multiple disease-related phenotypes. Results: We applied this method to two large, well-characterized studies of chronic obstructive pulmonary disease (COPD). We also examined the associations between these COPD phenotypic networks and other factors, including case-control status, disease severity, and genetic variants. Using these phenotypic networks, we have detected novel relationships between phenotypes that would not have been observed using traditional epidemiological approaches. Conclusion: Phenotypic network analysis of complex diseases could provide novel insights into disease susceptibility, disease severity, and genetic mechanisms

Allocentric versus egocentric spatial memory in autism spectrum disorder

Individuals with Autism Spectrum Disorder (ASD) present difficulties in forming relations among items and context. This capacity for relational binding is also involved in spatial navigation and research on this topic in ASD is scarce and inconclusive. Using a computerised version of the Morris Water Maze task, ASD participants showed particular difficulties in performing viewpoint independent (allocentric) navigation, leaving viewpoint dependent navigation (egocentric) intact. Further analyses showed that navigation deficits were not related to poor visual short-term memory or mental rotation in the ASD group. The results further confirm the need of autistic individuals for support at retrieval and have important implications for the design of signposts and maps