3,177 research outputs found
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data
Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.
Calogero-Moser models with noncommutative spin interactions
We construct integrable generalizations of the elliptic
Calogero-Sutherland-Moser model of particles with spin, involving
noncommutative spin interactions. The spin coupling potential is a modular
function and, generically, breaks the global spin symmetry of the model down to
a product of U(1) phase symmetries. Previously known models are recovered as
special cases.Comment: Version to appear in Phys. Rev. Let
Reflectionless tunneling in ballistic normal-metal--superconductor junctions
We investigate the phenomenon of reflectionless tunneling in ballistic
normal-metal--superconductor (NS) structures, using a semiclassical formalism.
It is shown that applied magnetic field and superconducting phase difference
both impair the constructive interference leading to this effect, but in a
qualitatively different way. This is manifested both in the conductance and in
the shot noise properties of the system considered. Unlike diffusive systems,
the features of the conductance are sharp, and enable fine spatial control of
the current, as well as single channel manipulations. We discuss the
possibility of conducting experiments in ballistic semiconductor-superconductor
structures with smooth interfaces and some of the phenomena, specific to such
structures, that could be measured. A general criterion for the barrier at NS
interfaces, though large, to be effectively transparent to pair current is
obtained.Comment: published versio
Probing photo-ionization: Experiments on positive streamers in pure gasses and mixtures
Positive streamers are thought to propagate by photo-ionization whose
parameters depend on the nitrogen:oxygen ratio. Therefore we study streamers in
nitrogen with 20%, 0.2% and 0.01% oxygen and in pure nitrogen, as well as in
pure oxygen and argon. Our new experimental set-up guarantees contamination of
the pure gases to be well below 1 ppm. Streamers in oxygen are difficult to
measure as they emit considerably less light in the sensitivity range of our
fast ICCD camera than the other gasses. Streamers in pure nitrogen and in all
nitrogen/oxygen mixtures look generally similar, but become somewhat thinner
and branch more with decreasing oxygen content. In pure nitrogen the streamers
can branch so much that they resemble feathers. This feature is even more
pronounced in pure argon, with approximately 10^2 hair tips/cm^3 in the
feathers at 200 mbar; this density could be interpreted as the free electron
density creating avalanches towards the streamer stem. It is remarkable that
the streamer velocity is essentially the same for similar voltage and pressure
in all nitrogen/oxygen mixtures as well as in pure nitrogen, while the oxygen
concentration and therefore the photo-ionization lengths vary by more than five
orders of magnitude. Streamers in argon have essentially the same velocity as
well. The physical similarity of streamers at different pressures is confirmed
in all gases; the minimal diameters are smaller than in earlier measurements.Comment: 28 pages, 14 figures. Major differences with v1: - appendix and
spectra removed - subsection regarding effects of repetition frequency added
- many more smaller change
Negative length orbits in normal-superconductor billiard systems
The Path-Length Spectra of mesoscopic systems including diffractive
scatterers and connected to superconductor is studied theoretically. We show
that the spectra differs fundamentally from that of normal systems due to the
presence of Andreev reflection. It is shown that negative path-lengths should
arise in the spectra as opposed to normal system. To highlight this effect we
carried out both quantum mechanical and semiclassical calculations for the
simplest possible diffractive scatterer. The most pronounced peaks in the
Path-Length Spectra of the reflection amplitude are identified by the routes
that the electron and/or hole travels.Comment: 4 pages, 4 figures include
Phase-sensitive quantum effects in Andreev conductance of the SNS system of metals with macroscopic phase breaking length
The dissipative component of electron transport through the doubly connected
SNS Andreev interferometer indium (S)-aluminium (N)-indium (S) has been
studied. Within helium temperature range, the conductance of the individual
sections of the interferometer exhibits phase-sensitive oscillations of
quantum-interference nature. In the non-domain (normal) state of indium
narrowing adjacent to NS interface, the nonresonance oscillations have been
observed, with the period inversely proportional to the area of the
interferometer orifice. In the domain intermediate state of the narrowing, the
magneto-temperature resistive oscillations appeared, with the period determined
by the coherence length in the magnetic field equal to the critical one. The
oscillating component of resonance form has been observed in the conductance of
the macroscopic N-aluminium part of the system. The phase of the oscillations
appears to be shifted by compared to that of nonresonance oscillations.
We offer an explanation in terms of the contribution into Josephson current
from the coherent quasiparticles with energies of order of the Thouless energy.
The behavior of dissipative transport with temperature has been studied in a
clean normal metal in the vicinity of a single point NS contact.Comment: 9 pages, 7 figures, to be published in Low Temp. Phys., v. 29, No.
12, 200
Abrupt appearance of the domain pattern and fatigue of thin ferroelectric films
We study the domain structure in ferroelectric thin films with a `passive'
layer (material with damaged ferroelectric properties) at the interface between
the film and electrodes within a continuous medium approximation. An abrupt
transition from a monodomain to a polydomain state has been found with the
increase of the `passive' layer thickness . The domain width changes very
quickly at the transition (exponentially with ). We have estimated the
dielectric response (the slope of the hysteresis loop) in the
`fatigued' multidomain state and found that it is in agreement with experiment,
assuming realistic parameters of the layer. We derive a simple universal
relation for the dielectric response, which scales as , involving only the
properties of the passive layer. This relation qualitatively reproduces the
evolution of the hysteresis loop in fatigued samples and it could be tested
with controlled experiments. It is expected that the coercive field should
increase with decreasing lateral size of the film. We believe that specific
properties of the domain structure under bias voltage in ferroelectrics with a
passive layer can resolve the long-standing `paradox of the coercive field'.Comment: 5 pages, REVTeX 3.1 with two eps-figures. Minor amendments. To appear
in Phys. Rev. Letter
A luminosity constraint on the origin of unidentified high energy sources
The identification of point sources poses a great challenge for the high
energy community. We present a new approach to evaluate the likelihood of a set
of sources being a Galactic population based on the simple assumption that
galaxies similar to the Milky Way host comparable populations of gamma-ray
emitters. We propose a luminosity constraint on Galactic source populations
which complements existing approaches by constraining the abundance and spatial
distribution of any objects of Galactic origin, rather than focusing on the
properties of a specific candidate emitter. We use M31 as a proxy for the Milky
Way, and demonstrate this technique by applying it to the unidentified EGRET
sources. We find that it is highly improbable that the majority of the
unidentified EGRET sources are members of a Galactic halo population (e.g.,
dark matter subhalos), but that current observations do not provide any
constraints on all of these sources being Galactic objects if they reside
entirely in the disk and bulge. Applying this method to upcoming observations
by the Fermi Gamma-ray Space Telescope has the potential to exclude association
of an even larger number of unidentified sources with any Galactic source
class.Comment: 18 pages, 4 figures, to appear in JPhys
- …