Towards an Algebra for Cascade Effects

We introduce a new class of (dynamical) systems that inherently capture cascading effects (viewed as consequential effects) and are naturally amenable to combinations. We develop an axiomatic general theory around those systems, and guide the endeavor towards an understanding of cascading failure. The theory evolves as an interplay of lattices and fixed points, and its results may be instantiated to commonly studied models of cascade effects. We characterize the systems through their fixed points, and equip them with two operators. We uncover properties of the operators, and express global systems through combinations of local systems. We enhance the theory with a notion of failure, and understand the class of shocks inducing a system to failure. We develop a notion of mu-rank to capture the energy of a system, and understand the minimal amount of effort required to fail a system, termed resilience. We deduce a dual notion of fragility and show that the combination of systems sets a limit on the amount of fragility inherited.Comment: 31 page

Stronger computational modelling of signalling pathways using both continuous and discrete-state methods

Starting from a biochemical signalling pathway model expresses in a process algebra enriched with quantitative information, we automatically derive both continuous-space and discrete-space representations suitable for numerical evaluation. We compare results obtained using approximate stochastic simulation thereby exposing a flaw in the use of the differentiation procedure producing misleading results

Computational and Mathematical Modelling of the EGF Receptor System

This chapter gives an overview of computational and mathematical modelling of the EGF receptor system. It begins with a survey of motivations for producing such models, then describes the main approaches that are taken to carrying out such modelling, viz. differential equations and individual-based modelling. Finally, a number of projects that applying modelling and simulation techniques to various aspects of the EGF receptor system are described

Geometrical statistics and vortex structures in helical and nonhelical turbulences

In this paper we conduct an analysis of the geometrical and vortical statistics in the small scales of helical and nonhelical turbulences generated with direct numerical simulations. Using a filtering approach, the helicity flux from large scales to small scales is represented by the subgrid-scale (SGS) helicity dissipation. The SGS helicity dissipation is proportional to the product between the SGS stress tensor and the symmetric part of the filtered vorticity gradient, a tensor we refer to as the vorticity strain rate. We document the statistics of the vorticity strain rate, the vorticity gradient, and the dual vector corresponding to the antisymmetric part of the vorticity gradient. These results provide new insights into the local structures of the vorticity field. We also study the relations between these quantities and vorticity, SGS helicity dissipation, SGS stress tensor, and other quantities. We observe the following in both helical and nonhelical turbulences: (1) there is a high probability to find the dual vector aligned with the intermediate eigenvector of the vorticity strain rate tensor; (2) vorticity tends to make an angle of 45 with both the most contractive and the most extensive eigendirections of the vorticity strain rate tensor; (3) the vorticity strain rate shows a preferred alignment configuration with the SGS stress tensor; (4) in regions with strong straining of the vortex lines, there is a negative correlation between the third order invariant of the vorticity gradient tensor and SGS helicity dissipation fluctuations. The correlation is qualitatively explained in terms of the self-induced motions of local vortex structures, which tend to wind up the vortex lines and generate SGS helicity dissipation. In helical turbulence, we observe that the joint probability density function of the second and third tensor invariants of the vorticity gradient displays skewed distributions, with the direction of skewness depending on the sign of helicity input. We also observe that the intermediate eigenvalue of the vorticity strain rate tensor is more probable to take negative values. These interesting observations, reported for the first time, call for further studies into their dynamical origins and implications. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3336012

Catastrophic regime shifts in model ecological communities are true phase transitions

Ecosystems often undergo abrupt regime shifts in response to gradual external changes. These shifts are theoretically understood as a regime switch between alternative stable states of the ecosystem dynamical response to smooth changes in external conditions. Usual models introduce nonlinearities in the macroscopic dynamics of the ecosystem that lead to different stable attractors among which the shift takes place. Here we propose an alternative explanation of catastrophic regime shifts based on a recent model that pictures ecological communities as systems in continuous fluctuation, according to certain transition probabilities, between different micro-states in the phase space of viable communities. We introduce a spontaneous extinction rate that accounts for gradual changes in external conditions, and upon variations on this control parameter the system undergoes a regime shift with similar features to those previously reported. Under our microscopic viewpoint we recover the main results obtained in previous theoretical and empirical work (anomalous variance, hysteresis cycles, trophic cascades). The model predicts a gradual loss of species in trophic levels from bottom to top near the transition. But more importantly, the spectral analysis of the transition probability matrix allows us to rigorously establish that we are observing the fingerprints, in a finite size system, of a true phase transition driven by background extinctions.Comment: 19 pages, 11 figures, revised versio

A closure theory for the split energy-helicity cascades in homogeneous isotropic homochiral turbulence

We study the energy transfer properties of three dimensional homogeneous and isotropic turbulence where the non-linear transfer is altered in a way that helicity is made sign-definite, say positive. In this framework, known as homochiral turbulence, an adapted eddy-damped quasi-normal Markovian (EDQNM) closure is derived to analyze the dynamics at very large Reynolds numbers, of order $10^5$ based on the Taylor scale. In agreement with previous findings, an inverse cascade of energy with a kinetic energy spectrum like $\propto k^{-5/3}$ is found for scales larger than the forcing one. Conjointly, a forward cascade of helicity towards larger wavenumbers is obtained, where the kinetic energy spectrum scales like $\propto k^{-7/3}$. By following the evolution of the closed spectral equations for a very long time and over a huge extensions of scales, we found the developing of a non monotonic shape for the front of the inverse energy flux. The very long time evolution of the kinetic energy and integral scale in both the forced and unforced cases is analyzed also.Comment: 8 pages, 3 figure

On the third order structure function for rotating 3D homogeneous turbulent flow

A form for the two-point third order structure function has been calculated for three dimensional homogeneous incompressible slowly rotating turbulent fluid. It has been argued that it may possibly hint at the initiation of the phenomenon of two-dimensionalisation of the 3D incompressible turbulence owing to rotation.Comment: This revised version corrects some serious flaws in the discussions after the equation (2) and the equation (13) of the earlier version. Some typos are also correcte