132 research outputs found
Quasi-Freestanding Multilayer Graphene Films on the Carbon Face of SiC
The electronic band structure of as-grown and doped graphene grown on the
carbon face of SiC is studied by high-resolution angle-resolved photoemission
spectroscopy, where we observe both rotations between adjacent layers and
AB-stacking. The band structure of quasi-freestanding AB- bilayers is directly
compared with bilayer graphene grown on the Si-face of SiC to study the impact
of the substrate on the electronic properties of epitaxial graphene. Our
results show that the C-face films are nearly freestanding from an electronic
point of view, due to the rotations between graphene layers.Comment: http://link.aps.org/doi/10.1103/PhysRevB.81.24141
Evaluation of conduction eigenchannels of an adatom probed by an STM tip
Ballistic conductance through a single atom adsorbed on a metallic surface
and probed by a scanning tunneling microscope (STM) tip can be decomposed into
eigenchannel contributions, which can be potentially obtained from shot noise
measurements. Our density functional theory calculations provide evidence that
transmission probabilities of these eigenchannels encode information on the
modifications of the adatom's local density of states caused by its interaction
with the STM tip. In the case of open shell atoms, this can be revealed in
nonmonotonic behavior of the eigenchannel's transmissions as a function of the
tip-adatom separation.Comment: 4.5 pages, 5 figures, REVTe
End-to-end learning of brain tissue segmentation from imperfect labeling
Segmenting a structural magnetic resonance imaging (MRI) scan is an important
pre-processing step for analytic procedures and subsequent inferences about
longitudinal tissue changes. Manual segmentation defines the current gold
standard in quality but is prohibitively expensive. Automatic approaches are
computationally intensive, incredibly slow at scale, and error prone due to
usually involving many potentially faulty intermediate steps. In order to
streamline the segmentation, we introduce a deep learning model that is based
on volumetric dilated convolutions, subsequently reducing both processing time
and errors. Compared to its competitors, the model has a reduced set of
parameters and thus is easier to train and much faster to execute. The contrast
in performance between the dilated network and its competitors becomes obvious
when both are tested on a large dataset of unprocessed human brain volumes. The
dilated network consistently outperforms not only another state-of-the-art deep
learning approach, the up convolutional network, but also the ground truth on
which it was trained. Not only can the incredible speed of our model make large
scale analyses much easier but we also believe it has great potential in a
clinical setting where, with little to no substantial delay, a patient and
provider can go over test results.Comment: Published as a conference paper at IJCNN 2017 Preprint versio
The Peculiarities of Large Intron Splicing in Animals
In mammals a considerable 92% of genes contain introns, with hundreds and hundreds of these introns reaching the incredible size of over 50,000 nucleotides. These “large introns” must be spliced out of the pre-mRNA in a timely fashion, which involves bringing together distant 5′ and 3′ acceptor and donor splice sites. In invertebrates, especially Drosophila, it has been shown that larger introns can be spliced efficiently through a process known as recursive splicing—a consecutive splicing from the 5′-end at a series of combined donor-acceptor splice sites called RP-sites. Using a computational analysis of the genomic sequences, we show that vertebrates lack the proper enrichment of RP-sites in their large introns, and, therefore, require some other method to aid splicing. We analyzed over 15,000 non-redundant, large introns from six mammals, 1,600 from chicken and zebrafish, and 560 non-redundant large introns from five invertebrates. Our bioinformatic investigation demonstrates that, unlike the studied invertebrates, the studied vertebrate genomes contain consistently abundant amounts of direct and complementary strand interspersed repetitive elements (mainly SINEs and LINEs) that may form stems with each other in large introns. This examination showed that predicted stems are indeed abundant and stable in the large introns of mammals. We hypothesize that such stems with long loops within large introns allow intron splice sites to find each other more quickly by folding the intronic RNA upon itself at smaller intervals and, thus, reducing the distance between donor and acceptor sites
Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA
Non-coding genomic regions in complex eukaryotes, including intergenic areas, introns, and untranslated segments of exons, are profoundly non-random in their nucleotide composition and consist of a complex mosaic of sequence patterns. These patterns include so-called Mid-Range Inhomogeneity (MRI) regions -- sequences 30-10000 nucleotides in length that are enriched by a particular base or combination of bases (e.g. (G+T)-rich, purine-rich, etc.). MRI regions are associated with unusual (non-B-form) DNA structures that are often involved in regulation of gene expression, recombination, and other genetic processes (Fedorova & Fedorov 2010). The existence of a strong fixation bias within MRI regions against mutations that tend to reduce their sequence inhomogeneity additionally supports the functionality and importance of these genomic sequences (Prakash et al. 2009)
Many-body interactions in quasi-freestanding graphene
The Landau-Fermi liquid picture for quasiparticles assumes that charge
carriers are dressed by many-body interactions, forming one of the fundamental
theories of solids. Whether this picture still holds for a semimetal like
graphene at the neutrality point, i.e., when the chemical potential coincides
with the Dirac point energy, is one of the long-standing puzzles in this field.
Here we present such a study in quasi-freestanding graphene by using
high-resolution angle-resolved photoemission spectroscopy. We see the
electron-electron and electron-phonon interactions go through substantial
changes when the semimetallic regime is approached, including renormalizations
due to strong electron-electron interactions with similarities to marginal
Fermi liquid behavior. These findings set a new benchmark in our understanding
of many-body physics in graphene and a variety of novel materials with Dirac
fermions.Comment: PNAS 2011 ; published ahead of print June 27, 201
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