Design and Development of Software Tools for Bio-PEPA

This paper surveys the design of software tools for the Bio-PEPA process algebra. Bio-PEPA is a high-level language for modelling biological systems such as metabolic pathways and other biochemical reaction networks. Through providing tools for this modelling language we hope to allow easier use of a range of simulators and model-checkers thereby freeing the modeller from the responsibility of developing a custom simulator for the problem of interest. Further, by providing mappings to a range of different analysis tools the Bio-PEPA language allows modellers to compare analysis results which have been computed using independent numerical analysers, which enhances the reliability and robustness of the results computed.

Discovery and Characterization of Transiting SuperEarths Using an All-Sky Transit Survey and Follow-up by the James Webb Space Telescope

Doppler and transit surveys are finding extrasolar planets of ever smaller mass and radius, and are now sampling the domain of superEarths (1-3 Earth radii). Recent results from the Doppler surveys suggest that discovery of a transiting superEarth in the habitable zone of a lower main sequence star may be possible. We evaluate the prospects for an all-sky transit survey targeted to the brightest stars, that would find the most favorable cases for photometric and spectroscopic characterization using the James Webb Space Telescope (JWST). We use the proposed Transiting Exoplanet Survey Satellite (TESS) as representative of an all-sky survey. We couple the simulated TESS yield to a sensitivity model for the MIRI and NIRSpec instruments on JWST. We focus on the TESS planets with radii between Earth and Neptune. Our simulations consider secondary eclipse filter photometry using JWST/MIRI, comparing the 11- and 15-micron bands to measure CO2 absorption in superEarths, as well as JWST/NIRSpec spectroscopy of water absorption from 1.7-3.0 microns, and CO2 absorption at 4.3-microns. We project that TESS will discover about eight nearby habitable transiting superEarths. The principal sources of uncertainty in the prospects for JWST characterization of habitable superEarths are superEarth frequency and the nature of superEarth atmospheres. Based on our estimates of these uncertainties, we project that JWST will be able to measure the temperature, and identify molecular absorptions (water, CO2) in one to four nearby habitable TESS superEarths.Comment: accepted for PASP; added discussion and figure for habitable planets; abridged Abstrac

Investigating modularity in the analysis of process algebra models of biochemical systems

Compositionality is a key feature of process algebras which is often cited as one of their advantages as a modelling technique. It is certainly true that in biochemical systems, as in many other systems, model construction is made easier in a formalism which allows the problem to be tackled compositionally. In this paper we consider the extent to which the compositional structure which is inherent in process algebra models of biochemical systems can be exploited during model solution. In essence this means using the compositional structure to guide decomposed solution and analysis. Unfortunately the dynamic behaviour of biochemical systems exhibits strong interdependencies between the components of the model making decomposed solution a difficult task. Nevertheless we believe that if such decomposition based on process algebras could be established it would demonstrate substantial benefits for systems biology modelling. In this paper we present our preliminary investigations based on a case study of the pheromone pathway in yeast, modelling in the stochastic process algebra Bio-PEPA

OGO-6 gas-surface energy transfer experiment

The kinetic energy flux of the upper atmosphere was analyzed using OGO-6 data. Energy transfer between 10 microwatts/sq cm and 0.1 W/sq cm was measured by short-term frequency changes of temperature-sensitive quartz crystals used in the energy transfer probe. The condition of the surfaces was continuously monitored by a quartz crystal microbalance to determine the effect surface contamination had on energy accommodation. Results are given on the computer analysis and laboratory tests performed to optimize the operation of the energy transfer probe. Data are also given on the bombardment of OGO-6 surfaces by high energy particles. The thermoelectrically-cooled quartz crystal microbalance is described in terms of its development and applications

Temporal behavior of the SO 1.707 micron ro-vibronic emission band in Io's atmosphere

We report observations of the ro-vibronic transition of SO at 1.707 microns on Io. These data were taken while Io was eclipsed by Jupiter, on four nights between July 2000 and March 2003. We analyze these results in conjunction with a previously published night to investigate the temporal behavior of these emissions. The observations were all conducted using the near-infrared spectrometer NIRSPEC on the W.M. Keck II telescope. The integrated emitted intensity for this band varies from 0.8 x 10^27 to 2.4 x 10^27 photons/sec, with a possible link to variations in Loki's infrared brightness. The band-shapes imply rotational temperatures of 550-1000K for the emitting gas, lending further evidence to a volcanic origin for sulfur monoxide. An attempt to detect the ro-vibronic transition of SO at 0.97 microns was unsuccessful; simultaneous detection with the 1.707 micron band would permit determination of the SO column abundance.Comment: 10 pages 4 figures. Accepted by Icarus 02/27/200

Effects of Bulk Composition on The Atmospheric Dynamics on Close-in Exoplanets

Super Earths and mini Neptunes likely have a wide range of atmospheric compositions, ranging from low-molecular mass atmospheres of H2 to higher molecular atmospheres of water, CO2, N2, or other species. Here, we systematically investigate the effects of atmospheric bulk compositions on temperature and wind distributions for tidally locked sub-Jupiter-sized planets, using an idealized 3D general circulation model (GCM). The bulk composition effects are characterized in the framework of two independent variables: molecular weight and molar heat capacity. The effect of molecular weight dominates. As the molecular weight increases, the atmosphere tends to have a larger day-night temperature contrast, a smaller eastward phase shift in the thermal phase curve and a smaller zonal wind speed. The width of the equatorial super-rotating jet also becomes narrower and the "jet core" region, where the zonal-mean jet speed maximizes, moves to a greater pressure level. The zonal-mean zonal wind is more prone to exhibit a latitudinally alternating pattern in a higher-molecular-weight atmosphere. We also present analytical theories that quantitatively explain the above trends and shed light on the underlying dynamical mechanisms. Those trends might be used to indirectly determine the atmospheric compositions on tidally locked sub-Jupiter-sized planets. The effects of the molar heat capacity are generally small. But if the vertical temperature profile is close to adiabatic, molar heat capacity will play a significant role in controlling the transition from a divergent flow in the upper atmosphere to a jet-dominated flow in the lower atmosphere.Comment: 25 pages, 22 figure

Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures

Here, using an integrative experimental and computational approach, Imle et al. show how cell motility and density affect HIV cell-associated transmission in a three-dimensional tissue-like culture system of CD4+ T cells and collagen, and how different collagen matrices restrict infection by cell-free virions