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