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 Li1−x_{1-x}Hx_xIO3_3 mixed crystals

A percolation model is proposed to explain the structural phase transitions found in Li$_{1-x}$H$_x$IO$_3$ mixed crystals as a function of the concentration parameter $x$. 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 $0.22 < x < 0.36$.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

Management of patients with increased risk for familial pancreatic cancer: updated recommendations from the International Cancer of the Pancreas Screening (CAPS) Consortium

Surgical oncolog