1,176 research outputs found
Spin-wave coupling to electromagnetic cavity fields in dysposium ferrite
Coupling of spin-waves with electromagnetic cavity field is demonstrated in
an antiferromagnet, dysprosium ferrite (DyFeO3). By measuring transmission at
0.2-0.35 THz and sweeping sample temperature, magnon-photon coupling signatures
were found at crossings of spin-wave resonances with Fabry-Perot cavity modes
formed in samples. The obtained spectra are explained in terms of classical
electrodynamics and a microscopic model.Comment: 3 pages, 2 figure
Diffusion, dimensionality and noise in transcriptional regulation
The precision of biochemical signaling is limited by randomness in the
diffusive arrival of molecules at their targets. For proteins binding to the
specific sites on the DNA and regulating transcription, the ability of the
proteins to diffuse in one dimension by sliding along the length of the DNA, in
addition to their diffusion in bulk solution, would seem to generate a larger
target for DNA binding, consequently reducing the noise in the occupancy of the
regulatory site. Here we show that this effect is largely cancelled by the
enhanced temporal correlations in one dimensional diffusion. With realistic
parameters, sliding along DNA has surprisingly little effect on the physical
limits to the precision of transcriptional regulation.Comment: 8 pages, 2 figure
Extending the dynamic range of transcription factor action by translational regulation
A crucial step in the regulation of gene expression is binding of
transcription factor (TF) proteins to regulatory sites along the DNA. But
transcription factors act at nanomolar concentrations, and noise due to random
arrival of these molecules at their binding sites can severely limit the
precision of regulation. Recent work on the optimization of information flow
through regulatory networks indicates that the lower end of the dynamic range
of concentrations is simply inaccessible, overwhelmed by the impact of this
noise. Motivated by the behavior of homeodomain proteins, such as the maternal
morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which
transcription factors also act as indirect translational regulators, binding to
the mRNA of other transcription factors. Intuitively, each mRNA molecule acts
as an independent sensor of the TF concentration, and averaging over these
multiple sensors reduces the noise. We analyze information flow through this
new scheme and identify conditions under which it outperforms direct
transcriptional regulation. Our results suggest that the dual role of
homeodomain proteins is not just a historical accident, but a solution to a
crucial physics problem in the regulation of gene expression.Comment: 14 pages, 5 figure
Information Optimization in Coupled Audio-Visual Cortical Maps
Barn owls hunt in the dark by using cues from both sight and sound to locate
their prey. This task is facilitated by topographic maps of the external space
formed by neurons (e.g., in the optic tectum) that respond to visual or aural
signals from a specific direction. Plasticity of these maps has been studied in
owls forced to wear prismatic spectacles that shift their visual field.
Adaptive behavior in young owls is accompanied by a compensating shift in the
response of (mapped) neurons to auditory signals. We model the receptive fields
of such neurons by linear filters that sample correlated audio-visual signals,
and search for filters that maximize the gathered information, while subject to
the costs of rewiring neurons. Assuming a higher fidelity of visual
information, we find that the corresponding receptive fields are robust and
unchanged by artificial shifts. The shape of the aural receptive field,
however, is controlled by correlations between sight and sound. In response to
prismatic glasses, the aural receptive fields shift in the compensating
direction, although their shape is modified due to the costs of rewiring.Comment: 7 pages, 1 figur
The thermodynamics of prediction
A system responding to a stochastic driving signal can be interpreted as
computing, by means of its dynamics, an implicit model of the environmental
variables. The system's state retains information about past environmental
fluctuations, and a fraction of this information is predictive of future ones.
The remaining nonpredictive information reflects model complexity that does not
improve predictive power, and thus represents the ineffectiveness of the model.
We expose the fundamental equivalence between this model inefficiency and
thermodynamic inefficiency, measured by dissipation. Our results hold
arbitrarily far from thermodynamic equilibrium and are applicable to a wide
range of systems, including biomolecular machines. They highlight a profound
connection between the effective use of information and efficient thermodynamic
operation: any system constructed to keep memory about its environment and to
operate with maximal energetic efficiency has to be predictive.Comment: 5 pages, 1 figur
Chemical Gradients in Galaxy Clusters and the Multiple Ways of Making a Cold Front
Cold fronts were originally interpreted as being the result of
subsonic/transonic motions of head-on merging substructures. This merger core
remnant model is theoretically justified and hold relatively well for clusters
that have clear signs of merging, such as 1E0657-56, but they do not work well
for the increasing number of cold fronts found in clusters that do not show
clear merging signs, such as A496. Here we report the results of a deeper
observation of that cluster that allowed us to produce high quality maps of the
gas parameters and to compare more closely the observations with the
predictions given by different models for cold front formation. We found for
the first time a ``cold arm'' characteristic of a flyby of a massive DM halo
near the core of the cluster. The cold arm is accompanied by an enhanced SN II
Fe mass fraction, inconsistent with the merger core remnant scenario.Comment: 3 pages, 1 figures, to appear in the Proceedings of "Heating vs.
Cooling in Galaxies and Clusters of Galaxies", August 2006, Garching
(Germany
Enhancement of the stability of genetic switches by overlapping upstream regulatory domains
We study genetic switches formed from pairs of mutually repressing operons.
The switch stability is characterised by a well defined lifetime which grows
sub-exponentially with the number of copies of the most-expressed transcription
factor, in the regime accessible by our numerical simulations. The stability
can be markedly enhanced by a suitable choice of overlap between the upstream
regulatory domains. Our results suggest that robustness against biochemical
noise can provide a selection pressure that drives operons, that regulate each
other, together in the course of evolution.Comment: 4 pages, 5 figures, RevTeX
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