Delays in Biological Regulatory Networks

International audienceIn this article, we propose a refinement of the modeling of genetic regulatory networks based on the approach of René Thomas. The notion of delays of activation/inhibition are added in order to specify which variable is faster affected by a change of its regulators. The formalism of linear hybrid automata is well suited to allow such refinement. We then use HyTech for two purposes: (1) to find automatically all paths from a specified initial state to another one and (2) to synthesize co nstraints on the delay parameters in order to follow any specific path

Charge transport in nanoscale vertical organic semiconductor pillar devices

We report charge transport measurements in nanoscale vertical pillar structures incorporating ultrathin layers of the organic semiconductor poly(3-hexylthiophene)(P3HT). P3HT layers with thickness down to 5 nm are gently top-contacted using wedging transfer, yielding highly reproducible, robust nanoscale junctions carrying high current densities (up to $10^6$ A/m$^2$). Current-voltage data modeling demonstrates excellent hole injection. This work opens up the pathway towards nanoscale, ultrashort-channel organic transistors for high-frequency and high-current-density operation.Comment: 30 pages, 8 figures, 1 tabl

Simulations of Dust in Interacting Galaxies I: Dust Attenuation

A new Monte-Carlo radiative-transfer code, Sunrise, is used in conjunction with hydrodynamic simulations of major galaxy mergers to calculate the effects of dust in such systems. The simulations are in good agreement with observations of dust absorption in starburst galaxies, and the dust has a profound effect on their appearance. The dust attenuation increases with luminosity such that at peak luminosities ~90% of the bolometric luminosity is absorbed by dust. In general, the detailed appearance of the merging event depends on the stage of the merger and the geometry of the encounter. The fraction of bolometric energy absorbed by the dust, however, is a robust quantity that can be predicted from the intrinsic properties bolometric luminosity, baryonic mass, star-formation rate, and metallicity of the system. This paper presents fitting formulae, valid over a wide range of masses and metallicities, from which the absorbed fraction of luminosity (and consequently also the infrared dust luminosity) can be predicted. The attenuation of the luminosity at specific wavelengths can also be predicted, albeit with a larger scatter due to the variation with viewing angle. These formulae for dust attenuation appear to be valid for both isolated and interacting galaxies, are consistent with earlier studies, and would be suitable for inclusion in theoretical models, e.g. semi-analytic models of galaxy formation.Comment: 12 pages, 10 figures, submitted to Ap

Gas Rich Dwarfs from the PSS-II III. HI Profiles and Dynamical Masses

We present Arecibo neutral hydrogen data on a sample of optically selected dwarf galaxies. The sample ranges in HI mass from 10^6 M_sun to 5x10^9 M_sun, with a mean of 7.9x10^8 M_sun. Using estimated HI radii, the HI surface densities range from 0.6 to 20 M_sun pc^-2, all well below the critical threshold for star formation (Kennicutt 1998). M_HI/L values of the LSB dwarfs range from 0.3 to 12 with a mean value of 2.0. Dynamical masses, calculated from the HI profile widths, range from 10^8 M_sun to 10^11 M_sun. There is a strong correlation between optical luminosity and dynamical mass for LSB dwarfs implying that the dark matter (whether baryonic or non-baryonic) follows the detectable baryonic matter.Comment: 53 pages, AASTeX v4.0, 8 figures, to be published in ApJ Suppl, images, tables and referee report can be found at http://zebu.uoregon.edu/~j

Towards a fully self-consistent spectral function of the nucleon in nuclear matter

We present a calculation of nuclear matter which goes beyond the usual quasi-particle approximation in that it includes part of the off-shell dependence of the self-energy in the self-consistent solution of the single-particle spectrum. The spectral function is separated in contributions for energies above and below the chemical potential. For holes we approximate the spectral function for energies below the chemical potential by a $\delta$-function at the quasi-particle peak and retain the standard form for energies above the chemical potential. For particles a similar procedure is followed. The approximated spectral function is consistently used at all levels of the calculation. Results for a model calculation are presented, the main conclusion is that although several observables are affected by the inclusion of the continuum contributions the physical consistency of the model does not improve with the improved self-consistency of the solution method. This in contrast to expectations based on the crucial role of self-consistency in the proofs of conservation laws.Comment: 26 pages Revtex with 4 figures, submitted to Phys. Rev.

Palaeoflow and Sediment Delivery Reconstructions from Martian Delta Morphology by Combined Modelling and HRSC DTM Analysis

have been formed by sapping. On the left of the delta there is a second lobe that may have formed as an initial drowned delta or alluvial fan. Summary: The size and shape of alluvial fans and deltas contain information on their formative time scale, sediment supply and the amount of water involved. A new numerical morphological model is presented that allows quantitative comparison of morphological predictions and HRSC DTMdata of six deltas. As morphology is uniquely coupled to water and sediment flux, the model also discriminates between dense flows (slurries) and dilute flows (rivers). We demonstrate that two Gilbert (Fig. 1) and three stepped fan deltas may have formed by dilute flows into filling lakes in less than 10 years. Introduction: Alluvial fans and deltas on Mars record past hydrological conditions. Until now these conditions were inferre

DDO 88: A Galaxy-Sized Hole in the Interstellar Medium

We present an HI and optical study of the gas-rich dwarf irregular galaxy DDO 88. Although DDO 88's global optical and HI parameters are normal for its morphological type, it hosts a large (3 kpc diameter) and unusually complete ring of enhanced HI emission. The gas ring is located at approximately one-third of the total HI radius and one-half the optically-defined Holmberg radius, and contains 30% of the total HI of the galaxy. The ring surrounds a central depression in the HI distribution, so it may be a shell formed by a starburst episode. However, the UBV colors in the HI hole are not bluer than the rest of the galaxy as would be expected if an unusual star-forming event had taken place there recently, but there is an old (~1-3 Gyr), red cluster near the center of the hole that is massive enough to have produced the hole in the HI. An age estimate for the ring, however, is uncertain because it is not observed to be expanding. An expansion model produces a lower estimate of 0.5 Gyr, but the presence of faint star formation regions associated with the ring indicate a much younger age. We also estimate that the ring could have dispersed by now if it is older than 0.5 Gyr. This implies that the ring is younger than 0.5 Gyr. A younger age would indicate that the red cluster did not produce the hole and ring. If this ring and the depression in the gas which it surrounds were not formed by stellar winds and supernovae, this would indicate that some other, currently unidentified, mechanism is operating.Comment: 44 pages; 16 figures. To appear in AJ, January 2005. Available from ftp.lowell.edu, cd pub/dah/papers/d88 and http://www.fiu.edu/~simpsonc/d8