34 research outputs found
Density-functional embedding using a plane-wave basis
The constrained electron density method of embedding a Kohn-Sham system in a
substrate system (first described by P. Cortona, Phys. Rev. B {\bf 44}, 8454
(1991) and T.A. Wesolowski and A. Warshel, J. Phys. Chem {\bf 97}, 8050 (1993))
is applied with a plane-wave basis and both local and non-local
pseudopotentials. This method divides the electron density of the system into
substrate and embedded electron densities, the sum of which is the electron
density of the system of interest. Coupling between the substrate and embedded
systems is achieved via approximate kinetic energy functionals. Bulk aluminium
is examined as a test case for which there is a strong interaction between the
substrate and embedded systems. A number of approximations to the
kinetic-energy functional, both semi-local and non-local, are investigated. It
is found that Kohn-Sham results can be well reproduced using a non-local
kinetic energy functional, with the total energy accurate to better than 0.1 eV
per atom and good agreement between the electron densities.Comment: 11 pages, 4 figure
Opening a new window to other worlds with spectropolarimetry
A high level of diversity has already been observed among the planets of our
own Solar System. As such, one expects extrasolar planets to present a wide
range of distinctive features, therefore the characterisation of Earth- and
super Earth-like planets is becoming of key importance in scientific research.
The SEARCH (Spectropolarimetric Exoplanet AtmospheRe CHaracerisation) mission
proposal of this paper represents one possible approach to realising these
objectives. The mission goals of SEARCH include the detailed characterisation
of a wide variety of exoplanets, ranging from terrestrial planets to gas
giants. More specifically, SEARCH will determine atmospheric properties such as
cloud coverage, surface pressure and atmospheric composition, and may also be
capable of identifying basic surface features. To resolve a planet with a semi
major axis of down to 1.4AU and 30pc distant SEARCH will have a mirror system
consisting of two segments, with elliptical rim, cut out of a parabolic mirror.
This will yield an effective diameter of 9 meters along one axis. A phase mask
coronagraph along with an integral spectrograph will be used to overcome the
contrast ratio of star to planet light. Such a mission would provide invaluable
data on the diversity present in extrasolar planetary systems and much more
could be learned from the similarities and differences compared to our own
Solar System. This would allow our theories of planetary formation, atmospheric
accretion and evolution to be tested, and our understanding of regions such as
the outer limit of the Habitable Zone to be further improved.Comment: 23 pages, accepted for publication in Experimental Astronom
A Continental-Wide Perspective: The Genepool of Nuclear Encoded Ribosomal DNA and Single-Copy Gene Sequences in North American Boechera (Brassicaceae)
74 of the currently accepted 111 taxa of the North American genus Boechera (Brassicaceae) were subject to pyhlogenetic reconstruction and network analysis. The dataset comprised 911 accessions for which ITS sequences were analyzed. Phylogenetic analyses yielded largely unresolved trees. Together with the network analysis confirming this result this can be interpreted as an indication for multiple, independent, and rapid diversification events. Network analyses were superimposed with datasets describing i) geographical distribution, ii) taxonomy, iii) reproductive mode, and iv) distribution history based on phylogeographic evidence. Our results provide first direct evidence for enormous reticulate evolution in the entire genus and give further insights into the evolutionary history of this complex genus on a continental scale. In addition two novel single-copy gene markers, orthologues of the Arabidopsis thaliana genes At2g25920 and At3g18900, were analyzed for subsets of taxa and confirmed the findings obtained through the ITS data
Agriculture productivity growth: Is the current trend on the track to poverty reduction?
Copyright © 2004 by Valenzuela, Ivanic, Ludena, and Hertel. All rights reserved.http://ageconsearch.umn.edu/handle/1915
Episignatures Stratifying Helsmoortel-Van Der Aa Syndrome Show Modest Correlation with Phenotype
none29siHelsmoortel-Van der Aa syndrome (HVDAS) is a neurodevelopmental condition associated with intellectual disability/developmental delay, autism spectrum disorder, and multiple medical comorbidities. HVDAS is caused by mutations in activity-dependent neuroprotective protein (ADNP). A recent study identified genome-wide DNA methylation changes in 22 individuals with HVDAS, adding to the group of neurodevelopmental disorders with an epigenetic signature. This methylation signature segregated those with HVDAS into two groups based on the location of the mutations. Here, we conducted an independent study on 24 individuals with HVDAS and replicated the existence of the two mutation-dependent episignatures. To probe whether the two distinct episignatures correlate with clinical outcomes, we used deep behavioral and neurobiological data from two prospective cohorts of individuals with a genetic diagnosis of HVDAS. We found limited phenotypic differences between the two HVDAS-affected groups and no evidence that individuals with more widespread methylation changes are more severely affected. Moreover, in spite of the methylation changes, we observed no profound alterations in the blood transcriptome of individuals with HVDAS. Our data warrant caution in harnessing methylation signatures in HVDAS as a tool for clinical stratification, at least with regard to behavioral phenotypes.noneBreen M.S.; Garg P.; Tang L.; Mendonca D.; Levy T.; Barbosa M.; Arnett A.B.; Kurtz-Nelson E.; Agolini E.; Battaglia A.; Chiocchetti A.G.; Freitag C.M.; Garcia-Alcon A.; Grammatico P.; Hertz-Picciotto I.; Ludena-Rodriguez Y.; Moreno C.; Novelli A.; Parellada M.; Pascolini G.; Tassone F.; Grice D.E.; Di Marino D.; Bernier R.A.; Kolevzon A.; Sharp A.J.; Buxbaum J.D.; Siper P.M.; De Rubeis S.Breen, M. S.; Garg, P.; Tang, L.; Mendonca, D.; Levy, T.; Barbosa, M.; Arnett, A. B.; Kurtz-Nelson, E.; Agolini, E.; Battaglia, A.; Chiocchetti, A. G.; Freitag, C. M.; Garcia-Alcon, A.; Grammatico, P.; Hertz-Picciotto, I.; Ludena-Rodriguez, Y.; Moreno, C.; Novelli, A.; Parellada, M.; Pascolini, G.; Tassone, F.; Grice, D. E.; Di Marino, D.; Bernier, R. A.; Kolevzon, A.; Sharp, A. J.; Buxbaum, J. D.; Siper, P. M.; De Rubeis, S