118 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
Modelling Non-linear Crowd Dynamics in Bio-PEPA
Emergent phenomena occur due to the pattern of non-linear and distributed local interactions between the elements of a system over time. Surprisingly, agent based crowd models, in which the movement of each individual follows a limited set of simple rules, often re-produce quite closely the emergent behaviour of crowds that can be observed in reality. An example of such phenomena is the spontaneous self-organisation of drinking parties in the squares of cities in Spain, also known as "El Botellon" [20]. We revisit this case study providing an elegant stochastic process algebraic model in Bio-PEPA amenable to several forms of analyses, among which simulation and fluid flow analysis. We show that a fluid flow approximation, i.e. a deterministic reading of the average behaviour of the system, can provide an alternative and efficient way to study the same emergent behaviour as that explored in [20] where simulation was used instead. Besides empirical evidence, also an analytical justification is provided for the good correspondence found between simulation results and the fluid flow approximation
Percolation model for structural phase transitions in LiHIO mixed crystals
A percolation model is proposed to explain the structural phase transitions
found in LiHIO mixed crystals as a function of the
concentration parameter . The percolation thresholds are obtained from Monte
Carlo simulations on the specific lattices occupied by lithium atoms and
hydrogen bonds. The theoretical results strongly suggest that percolating
lithium vacancies and hydrogen bonds are indeed responsible for the solid
solution observed in the experimental range .Comment: 4 pages, 2 figure
Massive Star Formation
This chapter reviews progress in the field of massive star formation. It
focuses on evidence for accretion and current models that invoke high accretion
rates. In particular it is noted that high accretion rates will cause the
massive young stellar object to have a radius much larger than its eventual
main sequence radius throughout much of the accretion phase. This results in
low effective temperatures which may provide the explanation as to why luminous
young stellar objects do not ionized their surroundings to form ultra-compact H
II regions. The transition to the ultra-compact H II region phase would then be
associated with the termination of the high accretion rate phase. Objects
thought to be in a transition phase are discussed and diagnostic diagrams to
distinguish between massive young stellar objects and ultra-compact H II
regions in terms of line widths and radio luminosity are presented.Comment: 21 pages, 6 figures, chapter in Diffuse Matter from Star Forming
Regions to Active Galaxies - A Volume Honouring John Dyson, Edited by T.W.
Hartquist, J. M. Pittard, and S. A. E. G. Falle. Series: Astrophysics and
Space Science Proceedings. Springer Dordrecht, 2007, p.6
How to move ionized gas: an introduction to the dynamics of HII regions
This review covers the dynamic processes that are important in the evolution
and structure of galactic HII regions, concentrating on an elementary
presentation of the physical concepts and recent numerical simulations of HII
region evolution in a non-uniform medium.
The contents are as follows:
(1) The equations (Euler equations; Radiative transfer; Rate equations; How
to avoid the dynamics; How to avoid the atomic physics).
(2) Physical concepts (Static photoionization equilibrium; Ionization front
propagation; Structure of a D-type front; Photoablation flows; Other
ingredients - Stellar winds, Radiation pressure, Magnetic fields,
Instabilities).
(3) HII region evolution (Early phases: hypercompact and ultracompact
regions; Later phases: compact and extended regions; Clumps and turbulence).Comment: To be published as a chapter in 'Diffuse Matter from Star Forming
Regions to Active Galaxies' - A volume Honouring John Dyson. Eds. T. W.
Harquist, J. M. Pittard and S. A. E. G. Falle. 25 pages, 7 figures. Some
figures degraded to meet size restriction. Full-resolution version available
at http://www.ifront.org/wiki/Dyson_Festschrift_Chapte
Fitting the integrated Spectral Energy Distributions of Galaxies
Fitting the spectral energy distributions (SEDs) of galaxies is an almost
universally used technique that has matured significantly in the last decade.
Model predictions and fitting procedures have improved significantly over this
time, attempting to keep up with the vastly increased volume and quality of
available data. We review here the field of SED fitting, describing the
modelling of ultraviolet to infrared galaxy SEDs, the creation of
multiwavelength data sets, and the methods used to fit model SEDs to observed
galaxy data sets. We touch upon the achievements and challenges in the major
ingredients of SED fitting, with a special emphasis on describing the interplay
between the quality of the available data, the quality of the available models,
and the best fitting technique to use in order to obtain a realistic
measurement as well as realistic uncertainties. We conclude that SED fitting
can be used effectively to derive a range of physical properties of galaxies,
such as redshift, stellar masses, star formation rates, dust masses, and
metallicities, with care taken not to over-interpret the available data. Yet
there still exist many issues such as estimating the age of the oldest stars in
a galaxy, finer details ofdust properties and dust-star geometry, and the
influences of poorly understood, luminous stellar types and phases. The
challenge for the coming years will be to improve both the models and the
observational data sets to resolve these uncertainties. The present review will
be made available on an interactive, moderated web page (sedfitting.org), where
the community can access and change the text. The intention is to expand the
text and keep it up to date over the coming years.Comment: 54 pages, 26 figures, Accepted for publication in Astrophysics &
Space Scienc
- …