Trend-based analysis of a population model of the AKAP scaffold protein

We formalise a continuous-time Markov chain with multi-dimensional discrete state space model of the AKAP scaffold protein as a crosstalk mediator between two biochemical signalling pathways. The analysis by temporal properties of the AKAP model requires reasoning about whether the counts of individuals of the same type (species) are increasing or decreasing. For this purpose we propose the concept of stochastic trends based on formulating the probabilities of transitions that increase (resp. decrease) the counts of individuals of the same type, and express these probabilities as formulae such that the state space of the model is not altered. We define a number of stochastic trend formulae (e.g. weakly increasing, strictly increasing, weakly decreasing, etc.) and use them to extend the set of state formulae of Continuous Stochastic Logic. We show how stochastic trends can be implemented in a guarded-command style specification language for transition systems. We illustrate the application of stochastic trends with numerous small examples and then we analyse the AKAP model in order to characterise and show causality and pulsating behaviours in this biochemical system

On variations of the brightness of type Ia supernovae with the age of the host stellar population

Recent observational studies of type Ia supernovae (SNeIa) suggest correlations between the peak brightness of an event and the age of the progenitor stellar population. This trend likely follows from properties of the progenitor white dwarf (WD), such as central density, that follow from properties of the host stellar population. We present a statistically well-controlled, systematic study utilizing a suite of multi-dimensional SNeIa simulations investigating the influence of central density of the progenitor WD on the production of Fe-group material, particularly radioactive Ni-56, which powers the light curve. We find that on average, as the progenitor's central density increases, production of Fe-group material does not change but production of Ni-56 decreases. We attribute this result to a higher rate of neutronization at higher density. The central density of the progenitor is determined by the mass of the WD and the cooling time prior to the onset of mass transfer from the companion, as well as the subsequent accretion heating and neutrino losses. The dependence of this density on cooling time, combined with the result of our central density study, offers an explanation for the observed age-luminosity correlation: a longer cooling time raises the central density at ignition thereby producing less Ni-56 and thus a dimmer event. While our ensemble of results demonstrates a significant trend, we find considerable variation between realizations, indicating the necessity for averaging over an ensemble of simulations to demonstrate a statistically significant result.Comment: 5 pages, 4 figures, 1 table, accepted to ApJ

Evaluating Systematic Dependencies of Type Ia Supernovae: The Influence of Deflagration to Detonation Density

We explore the effects of the deflagration to detonation transition (DDT) density on the production of Ni-56 in thermonuclear supernova explosions (type Ia supernovae). Within the DDT paradigm, the transition density sets the amount of expansion during the deflagration phase of the explosion and therefore the amount of nuclear statistical equilibrium (NSE) material produced. We employ a theoretical framework for a well-controlled statistical study of two-dimensional simulations of thermonuclear supernovae with randomized initial conditions that can, with a particular choice of transition density, produce a similar average and range of Ni-56 masses to those inferred from observations. Within this framework, we utilize a more realistic "simmered" white dwarf progenitor model with a flame model and energetics scheme to calculate the amount of Ni-56 and NSE material synthesized for a suite of simulated explosions in which the transition density is varied in the range 1-3x10^7 g/cc. We find a quadratic dependence of the NSE yield on the log of the transition density, which is determined by the competition between plume rise and stellar expansion. By considering the effect of metallicity on the transition density, we find the NSE yield decreases by 0.055 +/- 0.004 solar masses for a 1 solar metallicity increase evaluated about solar metallicity. For the same change in metallicity, this result translates to a 0.067 +/- 0.004 solar mass decrease in the Ni-56 yield, slightly stronger than that due to the variation in electron fraction from the initial composition. Observations testing the dependence of the yield on metallicity remain somewhat ambiguous, but the dependence we find is comparable to that inferred from some studies.Comment: 15 pages, 13 figures, accepted to ApJ on July 6, 201

Numerical Models of Binary Neutron Star System Mergers. I.: Numerical Methods and Equilibrium Data for Newtonian Models

The numerical modeling of binary neutron star mergers has become a subject of much interest in recent years. While a full and accurate model of this phenomenon would require the evolution of the equations of relativistic hydrodynamics along with the Einstein field equations, a qualitative study of the early stages on inspiral can be accomplished by either Newtonian or post-Newtonian models, which are more tractable. In this paper we offer a comparison of results from both rotating and non-rotating (inertial) frame Newtonian calculations. We find that the rotating frame calculations offer significantly improved accuracy as compared with the inertial frame models. Furthermore, we show that inertial frame models exhibit significant and erroneous angular momentum loss during the simulations that leads to an unphysical inspiral of the two neutron stars. We also examine the dependence of the models on initial conditions by considering initial configurations that consist of spherical neutron stars as well as stars that are in equilibrium and which are tidally distorted. We compare our models those of Rasio & Shapiro (1992,1994a) and New & Tohline (1997). Finally, we investigate the use of the isolated star approximation for the construction of initial data.Comment: 32 pages, 19 gif figures, manuscript with postscript figures available at http://www.astro.sunysb.edu/dswesty/docs/nspap1.p

Winter Conditions Influence Biological Responses of Migrating Hummingbirds

Conserving biological diversity given ongoing environmental changes requires the knowledge of how organisms respond biologically to these changes; however, we rarely have this information. This data deficiency can be addressed with coordinated monitoring programs that provide field data across temporal and spatial scales and with process-based models, which provide a method for predicting how species, in particular migrating species that face different conditions across their range, will respond to climate change. We evaluate whether environmental conditions in the wintering grounds of broad-tailed hummingbirds influence physiological and behavioral attributes of their migration. To quantify winter ground conditions, we used operative temperature as a proxy for physiological constraint, and precipitation and the normalized difference vegetation index (NDVI) as surrogates of resource availability. We measured four biological response variables: molt stage, timing of arrival at stopover sites, body mass, and fat. Consistent with our predictions, we found that birds migrating north were in earlier stages of molt and arrived at stopover sites later when NDVI was low. These results indicate that wintering conditions impact the timing and condition of birds as they migrate north. In addition, our results suggest that biologically informed environmental surrogates provide a valuable tool for predicting how climate variability across years influences the animal populations