1,950 research outputs found
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
Spin and orbital dynamics through the metal-to-insulator transition in CdOsO probed with high-resolution RIXS
High-resolution resonant inelastic x-ray scattering (RIXS) measurements
(E = 46 meV) have been performed on CdOsO through the
metal-to-insulator transition (MIT). A magnetic excitation at 125 meV evolves
continuously through the MIT, in agreement with recent Raman scattering
results, and provides further confirmation for an all-in, all-out magnetic
ground state. Asymmetry of this feature is likely a result of coupling between
the electronic and magnetic degrees of freedom. We also observe a broad
continuum of interband excitations centered at 0.3 eV energy loss. This is
indicative of significant hybridization between Os 5 and O 2 states, and
concurrent itinerant nature of the system. In turn, this suggests a possible
break down of the free-ion model for CdOsO.Comment: Accepted in Physical Review B (10 pages
Flame Evolution During Type Ia Supernovae and the Deflagration Phase in the Gravitationally Confined Detonation Scenario
We develop an improved method for tracking the nuclear flame during the
deflagration phase of a Type Ia supernova, and apply it to study the variation
in outcomes expected from the gravitationally confined detonation (GCD)
paradigm. A simplified 3-stage burning model and a non-static ash state are
integrated with an artificially thickened advection-diffusion-reaction (ADR)
flame front in order to provide an accurate but highly efficient representation
of the energy release and electron capture in and after the unresolvable flame.
We demonstrate that both our ADR and energy release methods do not generate
significant acoustic noise, as has been a problem with previous ADR-based
schemes. We proceed to model aspects of the deflagration, particularly the role
of buoyancy of the hot ash, and find that our methods are reasonably
well-behaved with respect to numerical resolution. We show that if a detonation
occurs in material swept up by the material ejected by the first rising bubble
but gravitationally confined to the white dwarf (WD) surface (the GCD
paradigm), the density structure of the WD at detonation is systematically
correlated with the distance of the deflagration ignition point from the center
of the star. Coupled to a suitably stochastic ignition process, this
correlation may provide a plausible explanation for the variety of nickel
masses seen in Type Ia Supernovae.Comment: 14 pages, 10 figures, accepted to the Astrophysical Journa
Process algebra modelling styles for biomolecular processes
We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed
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