Oscillations in the expression of a self-repressed gene induced by a slow transcriptional dynamics

We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of sustained oscillations and find that they require degradation mechanisms much less nonlinear than for infinitely fast regulation. Deterministic predictions are also compared with stochastic simulations of this minimal genetic oscillator

Oscillations in the expression of a self-repressed gene induced by a slow transcriptional dynamics

We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of sustained oscillations and find that they require degradation mechanisms much less nonlinear than for infinitely fast regulation. Deterministic predictions are also compared with stochastic simulations of this minimal genetic oscillator

A Non-parametric Semi-supervised Discretization Method

Semi-supervised classification methods aim to exploit labelled and unlabelled examples to train a predictive model. Most of these approaches make assumptions on the distribution of classes. This article first proposes a new semi-supervised discretization method which adopts very low informative prior on data. This method discretizes the numerical domain of a continuous input variable, while keeping the information relative to the prediction of classes. Then, an in-depth comparison of this semi-supervised method with the original supervised MODL approach is presented. We demonstrate that the semi-supervised approach is asymptotically equivalent to the supervised approach, improved with a post-optimization of the intervals bounds location

The Excitation of Extended Red Emission: New Constraints on its Carrier From HST Observations of NGC 7023

The carrier of the dust-associated photoluminescence process causing the extended red emission (ERE) in many dusty interstellar environments remains unidentified. Several competing models are more or less able to match the observed broad, unstructured ERE band. We now constrain the character of the ERE carrier further by determining the wavelengths of the radiation that initiates the ERE. Using the imaging capabilities of the Hubble Space Telescope, we have resolved the width of narrow ERE filaments appearing on the surfaces of externally illuminated molecular clouds in the bright reflection nebula NGC 7023 and compared them with the depth of penetration of radiation of known wavelengths into the same cloud surfaces. We identify photons with wavelengths shortward of 118 nm as the source of ERE initiation, not to be confused with ERE excitation, however. There are strong indications from the well-studied ERE in the Red Rectangle nebula and in the high-|b| Galactic cirrus that the photon flux with wavelengths shortward of 118 nm is too small to actually excite the observed ERE, even with 100% quantum efficiency. We conclude, therefore, that ERE excitation results from a two-step process. While none of the previously proposed ERE models can match these new constraints, we note that under interstellar conditions most polycyclic aromatic hydrocarbon (PAH) molecules are ionized to the di-cation stage by photons with E > 10.5 eV and that the electronic energy level structure of PAH di-cations is consistent with fluorescence in the wavelength band of the ERE. Therefore, PAH di-cations deserve further study as potential carriers of the ERE. (abridged)Comment: Accepted for Publication in the Ap

Apparent yield stress in rigid fibre suspensions: the role of attractive colloidal interactions

International audienceThis work is focused on the modelling of the shear and normal stresses in fibre suspensions that are subjected to a simple shear flow in the presence of short-range lubrication forces, van der Waals and electrostatic forces, as well as solid friction forces between fibres. All these forces are weighed by the contact probability. The theory is developed for attractive fibres with van der Waals interaction dominating over electrostatic repulsion. The model predicts a simple Bingham law for both the shear stress and the first normal stress difference with the apparent shear and normal yield stresses proportional, respectively, to the second and the third power of particle volume fraction. The model is applied to the experimental data of Rakatekar et al. Adv. Mater 21, 874-878 (2009) and Natale et al. AIChE J. 60, 1476-1487 (2014) on the suspensions of carbon nanotubes dispersed in a Newtonian epoxy resin. It reproduces well the quadratic dependency of the apparent yield stress on particle volume fraction (σ Y ∝φ^2) for average particle aspect ratios of r=160 and 1200, while it underpredicts the power-law exponent for rD80 (always predictingφ^2 behaviour instead of φ^3.2

Phonons and Colossal Thermal Expansion Behavior of Ag3Co(CN)6 and Ag3Fe(CN)6

Recently colossal positive volume thermal expansion has been found in the framework compounds Ag3Co(CN)6 and Ag3Fe(CN)6. Phonon spectra have been measured using the inelastic neutron scattering technique as a function of temperature and pressure. The data has been analyzed using ab-initio calculations. We find that the bonding is very similar in both compounds. At ambient pressure modes in the intermediate frequency part of the vibrational spectra in the Co compound are shifted to slightly higher energies as compared to the Fe compound. The temperature dependence of the phonon spectra gives evidence for large explicit anharmonic contribution to the total anharmonicity for low-energy modes below 5 meV. We found that modes are mainly affected by the change in the size of unit cell, which in turn changes the bond lengths and vibrational frequencies. Thermal expansion has been calculated via the volume dependence of phonon spectra. Our analysis indicates that Ag phonon modes in the energy range from 2 to 5 meV are strongly anharmonic and major contributors to thermal expansion in both compounds. The application of pressure hardens the low-energy part of the phonon spectra involving Ag vibrations and confirms the highly anharmonic nature of these modes.Comment: 19 pages, 14 figures and one tabl

Dust Emission Features in NGC 7023 between 0.35 and 2.5 micron: Extended Red Emission (0.7 micron) and Two New Emission Features (1.15 and 1.5 micron)

We present 0.35 to 2.5 micron spectra of the south and northwest filaments in the reflection nebula NGC 7023. These spectra were used to test the theory of Seahra & Duley that carbon nanoparticles are responsible for Extended Red Emission (ERE). Our spectra fail to show their predicted second emission band at 1.0 micron even though both filaments exhibit strong emission in the familiar 0.7 micron ERE band. The northwest filament spectrum does show one, and possibly two, new dust emission features in the near-infrared. We clearly detect a strong emission band at 1.5 micron which we tentatively attribute to beta-FeSi_2 grains. We tentatively detect a weaker emission band at 1.15 micron which coincides with the location expected for transitions from the conduction band to mid-gap defect states of silicon nanoparticles. This is added evidence that silicon nanoparticles are responsible for ERE as they already can explain the observed behavior of the main visible ERE band.Comment: 9 pages, color figures, accepted to the ApJ, color and b/w versions available at http://dirty.as.arizona.edu/~kgordon/papers/ere_1um.htm

Near-Infrared Spectroscopy of Molecular Filaments in the Reflection Nebula NGC 7023

We present near-infrared spectroscopy of fluorescent molecular hydrogen (H_2) emission from molecular filaments in the reflection nebula NGC 7023. We derive the relative column densities of H_2 rotational-vibrational states from the measured line emission and compare these results with several model photodissociation regions covering a range of densities, incident UV-fields, and excitation mechanisms. Our best-fit models for one filament suggest, but do not require, either a combination of different densities, suggesting clumps of 10^6 cm^{-3} in a 10^4 - 10^5 cm^{-3} filament, or a combination of fluorescent excitation and thermally-excited gas, perhaps due to a shock from a bipolar outflow. We derive densities and UV fields for these molecular filaments that are in agreement with previous determinations.Comment: ApJ accepted, 26 pages including 5 embedded figures, uses AASTEX. Also available at http://www-astronomy.mps.ohio-state.edu/~martini/pubs.htm