Analysis of signalling pathways using continuous time Markov chains

We describe a quantitative modelling and analysis approach for signal transduction networks. We illustrate the approach with an example, the RKIP inhibited ERK pathway [CSK+03]. Our models are high level descriptions of continuous time Markov chains: proteins are modelled by synchronous processes and reactions by transitions. Concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis such as what is the probability that if a concentration reaches a certain level, it will remain at that level thereafter? or how does varying a given reaction rate affect that probability? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

On the role of the H2 ortho:para ratio in gravitational collapse during star formation

Hydrogen molecules (H2) come in two forms in the interstellar medium, ortho- and para-hydrogen, corresponding to the two different spin configurations of the two hydrogen atoms. The relative abundances of the two flavours in the interstellar medium are still very uncertain, and this abundance ratio has a significant impact on the thermal properties of the gas. In the context of star formation, theoretical studies have recently adopted two different strategies when considering the ortho:para ratio (OPR) of H2 molecules; the first considers the OPR to be frozen at 3:1 while the second assumes that the species are in thermal equilibrium. As the OPR potentially affects the protostellar cores which form as a result of the gravitational collapse of a dense molecular cloud, the aim of this paper is to quantify precisely what role the choice of OPR plays in the properties and evolution of the cores. We used two different ideal gas equations of state for a hydrogen and helium mix in a radiation hydrodynamics code to simulate the collapse of a dense cloud and the formation of the first and second Larson cores; the first equation of state uses a fixed OPR of 3:1 while the second assumes thermal equilibrium. Simulations using an equilibrium ratio collapse faster at early times and show noticeable oscillations around hydrostatic equilibrium, to the point where the core expands for a short time right after its formation before resuming its contraction. In the case of a fixed 3:1 OPR, the core's evolution is a lot smoother. The OPR was however found to have little impact on the size, mass and radius of the two Larson cores. We conclude that if one is solely interested in the final properties of the cores when they are formed, it does not matter which OPR is used. On the other hand, if one's focus lies primarily in the evolution of the first core, the choice of OPR becomes important.The research leading to these results has received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007−2013 Grant Agreement No. 247060). K.T. is supported by Japan Society for the Promotion of Science (JSPS) Postdoctoral Fellowship for Research Abroad. The authors would also like to thank the anonymous referee for useful comments

Atmospheres and Spectra of Strongly Magnetized Neutron Stars -- III. Partially Ionized Hydrogen Models

We construct partially ionized hydrogen atmosphere models for magnetized neutron stars in radiative equilibrium with surface fields B=10^12-5 \times 10^14 G and effective temperatures T_eff \sim a few \times 10^5-10^6 K. These models are based on the latest equation of state and opacity results for magnetized, partially ionized hydrogen plasmas that take into account various magnetic and dense medium effects. The atmospheres directly determine the characteristics of thermal emission from isolated neutron stars. For the models with B=10^12-10^13 G, the spectral features due to neutral atoms lie at extreme UV and very soft X-ray energy bands and therefore are difficult to observe. However, the continuum flux is also different from the fully ionized case, especially at lower energies. For the superstrong field models (B\ga 10^14 G), we show that the vacuum polarization effect not only suppresses the proton cyclotron line as shown previously, but also suppresses spectral features due to bound species; therefore spectral lines or features in thermal radiation are more difficult to observe when the neutron star magnetic field is \ga 10^14 G.Comment: 12 pages, 10 figures; ApJ, accepted (v599: Dec 20, 2003

On the Correlation between the Magnetic Activity Levels, the Metallicities and the Radii of Low-Mass Stars

The recent burst in the number of radii measurements of very low-mass stars from eclipsing binaries and interferometry of single stars has opened more questions about what can be causing the discrepancy between the observed radii and the ones predicted by the models. The two main explanations being proposed are a correlation between the radius of the stars and their activity levels or their metallicities. This paper presents a study of such correlations using all the data published to date. The study also investigates correlations between the radii deviation from the models and the masses of the stars. There is no clear correlation between activity level and radii for the single stars in the sample. Those single stars are slow rotators with typical velocities v_rot sini < 3.0 km s^-1. A clear correlation however exists in the case of the faster rotating members of binaries. This result is based on the of X-ray emission levels of the stars. There also appears to be an increase in the deviation of the radii of single stars from the models as a function of metallicity, as previously indicated by Berger et al. (2006). The stars in binaries do not seem to follow the same trend. Finally, the Baraffe et al. (1998) models reproduce well the radius observations below 0.30-0.35Msun, where the stars become fully convective, although this result is preliminary since almost all the sample stars in that mass range are slow rotators and metallicities have not been measured for most of them. The results in this paper indicate that stellar activity and metallicity play an important role on the determination of the radius of very low-mass stars, at least above 0.35Msun.Comment: 22 pages, 4 figures. Accepted for publication on Ap

Protostellar birth with ambipolar and ohmic diffusion

This is the final version of the article. Available from EDP Sciences via the DOI in this record.The transport of angular momentum is capital during the formation of low-mass stars; too little removal and rotation ensures stellar densities are never reached, too much and the absence of rotation means no protoplanetary disks can form. Magnetic diffusion is seen as a pathway to resolving this long-standing problem. We investigate the impact of including resistive MHD in simulations of the gravitational collapse of a 1 solar mass gas sphere, from molecular cloud densities to the formation of the protostellar seed; the second Larson core. We used the AMR code RAMSES to perform two 3D simulations of collapsing magnetised gas spheres, including self-gravity, radiative transfer, and a non-ideal gas equation of state to describe H2 dissociation which leads to the second collapse. The first run was carried out under the ideal MHD approximation, while ambipolar and ohmic diffusion was incorporated in the second calculation. In the ideal MHD simulation, the magnetic field dominates the energy budget everywhere inside and around the first core, fueling interchange instabilities and driving a low-velocity outflow. High magnetic braking removes essentially all angular momentum from the second core. On the other hand, ambipolar and ohmic diffusion create a barrier which prevents amplification of the magnetic field beyond 0.1 G in the first Larson core which is now fully thermally supported. A significant amount of rotation is preserved and a small Keplerian-like disk forms around the second core. When studying the radiative efficiency of the first and second core accretion shocks, we found that it can vary by several orders of magnitude over the 3D surface of the cores. Magnetic diffusion is a pre-requisite to star-formation; it enables the formation of protoplanetary disks in which planets will eventually form, and also plays a determinant role in the formation of the protostar itself.We are indebted to the anonymous referee for his/her insightful comments that have vastly improved the solidity of our study, with no stones left unturned. We also thank Troels Haugbølle for very useful discussions during the writing of this paper. NV gratefully acknowledges support from the European Commission through the Horizon 2020 Marie Skłodowska-Curie Actions Individual Fellowship 2014 programme (Grant Agreement no. 659706). The research leading to these results has also received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013 Grant Agreement no. 247060). We acknowledge financial support from "Programme National de Physique Stellaire" (PNPS) of CNRS/INSU, CEA and CNES, France. This work was granted access to the HPC resources of CINES (Occigen) under the allocation 2016-047247 made by GENCI. We also made use of the astrophysics HPC facility at the University of Copenhagen, which is supported by a research grant (VKR023406) from Villum Fonden. In addition, we thank the Service d’Astrophysique, IRFU, CEA Saclay, and the Laboratoire Astrophysique Instrumentation Modélisation, France, for granting us access to the supercomputer IRFUCOAST where the groundwork with many test calculations were performed. All the figures were created using the OSIRIS8 visualization package for RAMSES, except Fig. 4 which was rendered with the PARAVIEW9 software

Epsilon Indi B: a new benchmark T dwarf

We have identified a new early T dwarf only 3.6pc from the Sun, as a common proper motion companion (separation 1459AU) to the K5V star Epsilon Indi (HD209100). As such, Epsilon Indi B is one of the highest proper motion sources outside the solar system (~4.7 arcsec/yr), part of one of the twenty nearest stellar systems, and the nearest brown dwarf to the Sun. Optical photometry obtained from the SuperCOSMOS Sky Survey was combined with approximate infrared photometry from the 2MASS Quicklook survey data release, yielding colours for the source typical of early T dwarfs. Follow up infrared spectroscopy using the ESO NTT and SOFI confirmed its spectral type to be T2.5+/-0.5. With Ks=11.2, Epsilon Indi B is 1.7 magnitudes brighter than any previously known T dwarf and 4 magnitudes brighter than the typical object in its class, making it highly amenable to detailed study. Also, as a companion to a bright nearby star, it has a precisely known distance (3.626pc) and relatively well-known age (0.8-2Gyr), allowing us to estimate its luminosity as logL/Lsun=-4.67, its effective temperature as 1260K, and its mass as ~40-60Mjup. Epsilon Indi B represents an important addition to the census of the Solar neighbourhood and, equally importantly, a new benchmark object in our understanding of substellar objects.Comment: Accepted by A&A (Letters); 5 pages, 3 figure

Forever Young: High Chromospheric Activity in M subdwarfs

We present spectroscopic observations of two halo M subdwarfs which have H alpha emission lines. We show that in both cases close companions are the most likely cause of the chromospheric activity in these old, metal-poor stars. We argue that Gl 781 A's unseen companion is most likely a cool helium white dwarf. Gl 455 is a near-equal-mass M subdwarf (sdM) system. Gl 781 A is rapidly rotating with v sin i = 30 km/s. The properties of the chromospheres and X-ray coronae of these systems are compared to M dwarfs with emission (dMe). The X-ray hardness ratios and optical chromospheric lines emission ratios are consistent with those seen in dMe stars. Comparison to active near-solar metallicity stars indicates that despite their low metallicity ([m/H] = -1/2), the sdMe stars are roughly as active in both X-rays and chromospheric emission. Measured by L_X/L_bol, the activity level of Gl 781 A is no more than a factor of 2.5 subluminous with respect to near-solar metallicity stars.Comment: 16 pages including 1 figure, AASTeX, to appear in May 1998 A.

Observations of Ultracool White Dwarfs

We present new spectroscopic and photometric measurements of the white dwarfs LHS 3250 and WD 0346+246. Along with F351-50, these white dwarfs are the coolest ones known, all with effective temperatures below 4000 K. Their membership in the Galactic halo population is discussed, and detailed comparisons of all three objects with new atmosphere models are presented. The new models consider the effects of mixed H/He atmospheres and indicate that WD 0346+246 and F351-50 have predominantly helium atmospheres with only traces of hydrogen. LHS 3250 may be a double degenerate whose average radiative temperature is between 2000 and 4000 K, but the new models fail to explain this object

Chemical solver to compute molecule and grain abundances and non-ideal MHD resistivities in prestellar core collapse calculations

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.We develop a detailed chemical network relevant to the conditions characteristic of prestellar core collapse. We solve the system of time-dependent differential equations to calculate the equilibrium abundances of molecules and dust grains, with a size distribution given by size-bins for these latter. These abundances are used to compute the different non-ideal magneto-hydrodynamics resistivities (ambipolar, Ohmic and Hall), needed to carry out simulations of protostellar collapse. For the first time in this context, we take into account the evaporation of the grains, the thermal ionisation of Potassium, Sodium and Hydrogen at high temperature, and the thermionic emission of grains in the chemical network, and we explore the impact of various cosmic ray ionisation rates. All these processes significantly affect the non-ideal magneto-hydrodynamics resistivities, which will modify the dynamics of the collapse. Ambipolar diffusion and Hall effect dominate at low densities, up to n_H = 10^12 cm^-3, after which Ohmic diffusion takes over. We find that the time-scale needed to reach chemical equilibrium is always shorter than the typical dynamical (free fall) one. This allows us to build a large, multi-dimensional multi-species equilibrium abundance table over a large temperature, density and ionisation rate ranges. This table, which we make accessible to the community, is used during first and second prestellar core collapse calculations to compute the non-ideal magneto-hydrodynamics resistivities, yielding a consistent dynamical-chemical description of this process