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

The Central Region in M100: Observations and Modeling

We present new high-resolution observations of the center of the late-type spiral M100 (NGC 4321) supplemented by 3D numerical modeling of stellar and gas dynamics, including star formation (SF). NIR imaging has revealed a stellar bar, previously inferred from optical and 21 cm observations, and an ovally-shaped ring-like structure in the plane of the disk. The K isophotes become progressively elongated and skewed to the position angle of the bar (outside and inside the `ring') forming an inner bar-like region. The galaxy exhibits a circumnuclear starburst in the inner part of the K `ring'. Two maxima of the K emission have been observed to lie symmetrically with respect to the nucleus and equidistant from it slightly leading the stellar bar. We interpret the twists in the K isophotes as being indicative of the presence of a double inner Lindblad resonance (ILR) and test this hypothesis by modeling the gas flow in a self-consistent gas + stars disk embedded in a halo, with an overall NGC4321-like mass distribution. We have reproduced the basic morphology of the region (the bar, the large scale trailing shocks, two symmetric K peaks corresponding to gas compression maxima which lie at the caustic formed by the interaction of a pair of trailing and leading shocks in the vicinity of the inner ILR, both peaks being sites of SF, and two additional zones of SF corresponding to the gas compression maxima, referred usually as `twin peaks').Comment: 31 pages, postscript, compressed, uuencoded. 21 figures available in postscript, compressed form by anonymous ftp from ftp://asta.pa.uky.edu/shlosman/main100 , mget *.ps.Z. To appear in Ap.

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.

Rotational Widths for Use in the Tully-Fisher Relation. II. The Impact of Surface Brightness

Using a large sample of spiral galaxies for which 21 cm single-dish and/or long-slit optical spectra are available, we make a detailed comparison between various estimates of rotational widths. Different optical width estimators are considered and their limitations discussed, with emphasis on biases associated with rotation curve properties (shape and extent) and disk central surface brightness. The best match with HI rotational velocities is obtained with Polyex widths, which are measured at the optical radius (encompassing a fixed fraction of the total light of the galaxy) from a model fit to the rotation curve. In contrast with Polyex widths, optical rotational velocities measured at 2.15 disk scale lengths r_d deviate from HI widths by an amount that correlates with the central surface brightness of the disk. This bias occurs because the rotation curves of galaxies are in general still rising at 2.15 r_d, and the fraction of total mass contained within this radius decreases with increasing disk surface brightness. Statistical corrections, parameterized by the radial extent of the observed rotation curve, are provided to reduce Polyex and HI width measurements into a homogeneous system. This yields a single robust estimate of rotational velocity to be used for applications of disk scaling relations.Comment: 13 pages, 8 figures. To appear in the Astronomical Journal (August 2007

LARCH Vogels Nationaal; een expertsysteem voor het beoordelen van de ruimtelijke samenhang en de duurzaamheid van broedvogelpopulaties in Nederland

Het model LARCH is een onderdeel van het kerninstrumentarium van het Natuurplanbureau. Het model voorspelt de kans op duurzaam voorkomen van vooral diersoorten op basis van de ruimtelijke configuratie van leefgebieden en de kwaliteit daarvan. Dit rapport beschrijft het toepasbaar maken van LARCH voor 89 broedvogelsoorten in Nederland, LARCH VOGELS NATIONAAL genaamd. Ten behoeve hiervan is een speciale begroeiingstypenkaart vervaardigd. Het model maakt deel uit van de Natuurplanner van het RIVM. De Natuurplanner integreert kennis over de effecten van de zogenoemde "ver"-thema's (verdroging, verzuring, vermesting) op planten en vegetatie(structuur). Door de uitbreiding met broedvogels kan ook de kennis over versnippering worden meegenomen

Galaxies with Spiral Structure up to z = 0.87 --Limits on M/L and the Stellar Velocity Dispersion

We consider seven distant galaxies with clearly evident spiral structure from HST images. Three of these were chosen from Vogt et al. (1996) (VFP) and have measured rotational velocities. Five were chosen from the Medium Deep Survey and are studied in Sarajedini et al. 1996 (SGGR), and one galaxy is found in both papers. We place upper limits on their mass-to-light ratios (M/L) by computing M/L_B for a maximal disk. We find that these galaxies have maximal disk mass-to-light ratios M/L_B = 1.5 - 3.5 M_sol/L_Bsol at the low end, but within the range seen in nearby galaxies. The mass-to-light ratios are low enough to suggest that the galaxies contain a young, rapidly formed stellar population. By using a Toomre stability criterion for formation of spiral structure, we place constraints on the ratio of M/L to the stellar velocity dispersion. If these galaxies have maximal disks they would have to be nearly unstable so as to have small enough velocity dispersions that their disks are not unrealistically thick. This suggests that there is a substantial amount of dark matter present in the luminous regions of the galaxy.Comment: AAS Latex + PS Figure, accepted for publication in A

Relativistic Brueckner-Hartree-Fock calculations with explicit intermediate negative energy states

In a relativistic Brueckner-Hartree-Fock calculation we include explicit negative-energy states in the two-body propagator. This is achieved by using the Gross spectator-equation, modified by medium effects. Qualitatively our results compare well with other RBHF calculations. In some details significant differences occur, e.g, our equation of state is stiffer and the momentum dependence of the self-energy components is stronger than found in a reference calculation without intermediate negative energy states.Comment: 13 pages Revtex, 5 figures included seperatel