647 research outputs found
Spontaneous membrane formation and self-encapsulation of active rods in an inhomogeneous motility field
We study the collective dynamics of self-propelled rods in an inhomogeneous
motility field. At the interface between two regions of constant but different
motility, a smectic rod layer is spontaneously created through aligning
interactions between the active rods, reminiscent of an artificial,
semi-permeable membrane. This "active membrane" engulfes rods which are locally
trapped in low-motility regions and thereby further enhances the trapping
efficiency by self-organization, an effect which we call "self-encapsulation".
Our results are gained by computer simulations of self-propelled rod models
confined on a two-dimensional planar or spherical surface with a stepwise
constant motility field, but the phenomenon should be observable in any
geometry with sufficiently large spatial inhomogeneity. We also discuss
possibilities to verify our predictions of active-membrane formation in
experiments of self-propelled colloidal rods and vibrated granular matter
A method for precise charge reconstruction with pixel detectors using binary hit information
A method is presented to precisely reconstruct charge spectra with pixel
detectors using binary hit information of individual pixels. The method is
independent of the charge information provided by the readout circuitry and has
a resolution mainly limited by the electronic noise. It relies on the ability
to change the detection threshold in small steps while counting hits from a
particle source. The errors are addressed and the performance of the method is
shown based on measurements with the ATLAS pixel chip FE-I4 bump bonded to a
230 {\mu}m 3D-silicon sensor. Charge spectra from radioactive sources and from
electron beams are presented serving as examples. It is demonstrated that a
charge resolution ({\sigma}<200 e) close to the electronic noise of the ATLAS
FE-I4 pixel chip can be achieved
Characterization and Verification Environment for the RD53A Pixel Readout Chip in 65 nm CMOS
The RD53 collaboration is currently designing a large scale prototype pixel
readout chip in 65 nm CMOS technology for the phase 2 upgrades at the HL-LHC.
The RD53A chip will be available by the end of the year 2017 and will be
extensively tested to confirm if the circuit and the architecture make a solid
foundation for the final pixel readout chips for the experiments at the HL-LHC.
A test and data acquisition system for the RD53A chip is currently under
development to perform single-chip and multi-chip module measurements. In
addition, the verification of the RD53A design is performed in a dedicated
simulation environment. The concept and the implementation of the test and data
acquisition system and the simulation environment, which are based on a modular
data acquisition and system testing framework, are presented in this work
Compaction dynamics in ductile granular media
Ductile compaction is common in many natural systems, but the temporal
evolution of such systems is rarely studied. We observe surprising oscillations
in the weight measured at the bottom of a self-compacting ensemble of ductile
grains. The oscillations develop during the first ten hours of the experiment,
and usually persist through the length of an experiment (one week). The weight
oscillations are connected to the grain--wall contacts, and are directly
correlated with the observed strain evolution and the dynamics of grain--wall
contacts during the compaction. Here, we present the experimental results and
characteristic time constants of the system, and discuss possible reasons for
the measured weight oscillations.Comment: 11 pages, 14 figure
Shape based indexing for faster search of RNA family databases
Janssen S, Reeder J, Giegerich R. Shape based indexing for faster search of RNA family databases. BMC Bioinformatics. 2008;9(1):131.Background: Most non-coding RNA families exert their function by means of a conserved, common secondary structure. The Rfam data base contains more than five hundred structurally annotated RNA families. Unfortunately, searching for new family members using covariance models (CMs) is very time consuming. Filtering approaches that use the sequence conservation to reduce the number of CM searches, are fast, but it is unknown to which sacrifice.
Results: We present a new filtering approach, which exploits the family specific secondary structure and significantly reduces the number of CM searches. The filter eliminates approximately 85% of the queries and discards only 2.6% true positives when evaluating Rfam against itself. First results also capture previously undetected non-coding RNAs in a recent human RNAz screen.
Conclusion: The RNA shape index filter (RNAsifter) is based on the following rationale: An RNA family is characterised by structure, much more succinctly than by sequence content. Structures of individual family members, which naturally have different length and sequence composition, may exhibit structural variation in detail, but overall, they have a common shape in a more abstract sense. Given a fixed release of the Rfam data base, we can compute these abstract shapes for all families. This is called a shape index. If a query sequence belongs to a certain family, it must be able to fold into the family shape with reasonable free energy. Therefore, rather than matching the query against all families in the data base, we can first (and quickly) compute its feasible shape(s), and use the shape index to access only those families where a good match is possible due to a common shape with the query
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