3,292 research outputs found
Novel application of query-based qualitative predictors for characterization of solvent accessible residues in conjunction with protein sequence homology. Proceedings of the 22nd International Workshop on Database and Expert Systems Applications
Can one reconstruct masked CMB sky?
The CMB maps obtained by observations always possess domains which have to be
masked due to severe uncertainties with respect to the genuine CMB signal.
Cosmological analyses ideally use full CMB maps in order to get e.g. the
angular power spectrum. There are attempts to reconstruct the masked regions at
least at low resolutions, i.e. at large angular scales, before a further
analysis follows. In this paper, the quality of the reconstruction is
investigated for the ILC (7yr) map as well as for 1000 CMB simulations of the
LambdaCDM concordance model. The latter allows an error estimation for the
reconstruction algorithm which reveals some drawbacks. The analysis points to
errors of the order of a significant fraction of the mean temperature
fluctuation of the CMB. The temperature 2-point correlation function C(theta)
is evaluated for different reconstructed sky maps which leads to the conclusion
that it is safest to compute it on the cut-sky
Coarse-graining protein energetics in sequence variables
We show that cluster expansions (CE), previously used to model solid-state
materials with binary or ternary configurational disorder, can be extended to
the protein design problem. We present a generalized CE framework, in which
properties such as energy can be unambiguously expanded in the amino-acid
sequence space. The CE coarse grains over nonsequence degrees of freedom (e.g.,
side-chain conformations) and thereby simplifies the problem of designing
proteins, or predicting the compatibility of a sequence with a given structure,
by many orders of magnitude. The CE is physically transparent, and can be
evaluated through linear regression on the energies of training sequences. We
show, as example, that good prediction accuracy is obtained with up to pairwise
interactions for a coiled-coil backbone, and that triplet interactions are
important in the energetics of a more globular zinc-finger backbone.Comment: 10 pages, 3 figure
Feasibility and performances of compressed-sensing and sparse map-making with Herschel/PACS data
The Herschel Space Observatory of ESA was launched in May 2009 and is in
operation since. From its distant orbit around L2 it needs to transmit a huge
quantity of information through a very limited bandwidth. This is especially
true for the PACS imaging camera which needs to compress its data far more than
what can be achieved with lossless compression. This is currently solved by
including lossy averaging and rounding steps on board. Recently, a new theory
called compressed-sensing emerged from the statistics community. This theory
makes use of the sparsity of natural (or astrophysical) images to optimize the
acquisition scheme of the data needed to estimate those images. Thus, it can
lead to high compression factors.
A previous article by Bobin et al. (2008) showed how the new theory could be
applied to simulated Herschel/PACS data to solve the compression requirement of
the instrument. In this article, we show that compressed-sensing theory can
indeed be successfully applied to actual Herschel/PACS data and give
significant improvements over the standard pipeline. In order to fully use the
redundancy present in the data, we perform full sky map estimation and
decompression at the same time, which cannot be done in most other compression
methods. We also demonstrate that the various artifacts affecting the data
(pink noise, glitches, whose behavior is a priori not well compatible with
compressed-sensing) can be handled as well in this new framework. Finally, we
make a comparison between the methods from the compressed-sensing scheme and
data acquired with the standard compression scheme. We discuss improvements
that can be made on ground for the creation of sky maps from the data.Comment: 11 pages, 6 figures, 5 tables, peer-reviewed articl
How well-proportioned are lens and prism spaces?
The CMB anisotropies in spherical 3-spaces with a non-trivial topology are
analysed with a focus on lens and prism shaped fundamental cells. The
conjecture is tested that well proportioned spaces lead to a suppression of
large-scale anisotropies according to the observed cosmic microwave background
(CMB). The focus is put on lens spaces L(p,q) which are supposed to be oddly
proportioned. However, there are inhomogeneous lens spaces whose shape of the
Voronoi domain depends on the position of the observer within the manifold.
Such manifolds possess no fixed measure of well-proportioned and allow a
predestined test of the well-proportioned conjecture. Topologies having the
same Voronoi domain are shown to possess distinct CMB statistics which thus
provide a counter-example to the well-proportioned conjecture. The CMB
properties are analysed in terms of cyclic subgroups Z_p, and new point of view
for the superior behaviour of the Poincar\'e dodecahedron is found
Long-Term Variations in the Growth and Decay Rates of Sunspot Groups
Using the combined Greenwich (1874-1976) and Solar Optical Observatories
Network (1977-2009) data on sunspot groups, we study the long-term variations
in the mean daily rates of growth and decay of sunspot groups. We find that the
minimum and the maximum values of the annually averaged daily mean growth rates
are ~52% per day and ~183% per day, respectively, whereas the corresponding
values of the annually averaged daily mean decay rates are ~21% per day and
~44% per day, respectively. The average value (over the period 1874-2009) of
the growth rate is about 70% more than that of the decay rate. The growth and
the decay rates vary by about 35% and 13%, respectively, on a 60-year
time-scale. From the beginning of Cycle 23 the growth rate is substantially
decreased and near the end (2007-2008) the growth rate is lowest in the past
about 100 years.Comment: 1 table, 13 figures, accepted by Solar Physic
Structural Synthesis for GXW Specifications
We define the GXW fragment of linear temporal logic (LTL) as the basis for
synthesizing embedded control software for safety-critical applications. Since
GXW includes the use of a weak-until operator we are able to specify a number
of diverse programmable logic control (PLC) problems, which we have compiled
from industrial training sets. For GXW controller specifications, we develop a
novel approach for synthesizing a set of synchronously communicating
actor-based controllers. This synthesis algorithm proceeds by means of
recursing over the structure of GXW specifications, and generates a set of
dedicated and synchronously communicating sub-controllers according to the
formula structure. In a subsequent step, 2QBF constraint solving identifies and
tries to resolve potential conflicts between individual GXW specifications.
This structural approach to GXW synthesis supports traceability between
requirements and the generated control code as mandated by certification
regimes for safety-critical software. Synthesis for GXW specifications is in
PSPACE compared to 2EXPTIME-completeness of full-fledged LTL synthesis. Indeed
our experimental results suggest that GXW synthesis scales well to
industrial-sized control synthesis problems with 20 input and output ports and
beyond.Comment: The long (including appendix) version being reviewed by CAV'16
program committee. Compared to the submitted version, one author (out of her
wish) is moved to the Acknowledgement. (v2) Corrected typos. (v3) Add an
additional remark over environment assumption and easy corner case
CMB Anisotropy of the Poincare Dodecahedron
We analyse the anisotropy of the cosmic microwave background (CMB) for the
Poincare dodecahedron which is an example for a multi-connected spherical
universe. We compare the temperature correlation function and the angular power
spectrum for the Poincare dodecahedral universe with the first-year WMAP data
and find that this multi-connected universe can explain the surprisingly low
CMB anisotropy on large scales found by WMAP provided that the total energy
density parameter Omega_tot is in the range 1.016...1.020. The ensemble average
over the primordial perturbations is assumed to be the scale-invariant
Harrison-Zel'dovich spectrum. The circles-in-the-sky signature is studied and
it is found that the signal of the six pairs of matched circles could be missed
by current analyses of CMB sky maps
CMB Anisotropy of Spherical Spaces
The first-year WMAP data taken at their face value hint that the Universe
might be slightly positively curved and therefore necessarily finite, since all
spherical (Clifford-Klein) space forms M^3 = S^3/Gamma, given by the quotient
of S^3 by a group Gamma of covering transformations, possess this property. We
examine the anisotropy of the cosmic microwave background (CMB) for all typical
groups Gamma corresponding to homogeneous universes. The CMB angular power
spectrum and the temperature correlation function are computed for the
homogeneous spaces as a function of the total energy density parameter
Omega_tot in the large range [1.01, 1.20] and are compared with the WMAP data.
We find that out of the infinitely many homogeneous spaces only the three
corresponding to the binary dihedral group T*, the binary octahedral group O*,
and the binary icosahedral group I* are in agreement with the WMAP
observations. Furthermore, if Omega_tot is restricted to the interval [1.00,
1.04], the space described by T* is excluded since it requires a value of
Omega_tot which is probably too large being in the range [1.06, 1.07]. We thus
conclude that there remain only the two homogeneous spherical spaces S^3/O* and
S^3/I* with Omega_tot of about 1.038 and 1.018, respectively, as possible
topologies for our Universe.Comment: A version with high resolution sky maps can be obtained at
http://www.physik.uni-ulm.de/theo/qc
Cosmic Topology of Polyhedral Double-Action Manifolds
A special class of non-trivial topologies of the spherical space S^3 is
investigated with respect to their cosmic microwave background (CMB)
anisotropies. The observed correlations of the anisotropies on the CMB sky
possess on large separation angles surprising low amplitudes which might be
naturally be explained by models of the Universe having a multiconnected
spatial space. We analysed in CQG 29(2012)215005 the CMB properties of prism
double-action manifolds that are generated by a binary dihedral group D^*_p and
a cyclic group Z_n up to a group order of 180. Here we extend the CMB analysis
to polyhedral double-action manifolds which are generated by the three binary
polyhedral groups (T^*, O^*, I^*) and a cyclic group Z_n up to a group order of
1000. There are 20 such polyhedral double-action manifolds. Some of them turn
out to have even lower CMB correlations on large angles than the Poincare
dodecahedron
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