15,194 research outputs found
Brane Calculi Systems: A Static Preview of their Possible Behaviour
We improve the precision of a previous Control Flow Analysis for Brane
Calculi, by adding information on the context and introducing causality
information on the membranes. This allows us to prove some biological
properties on the behaviour of systems specified in Brane Calculi.Comment: Presented at MeCBIC 201
Causal interactions and delays in a neuronal ensemble
We analyze a neural system which mimics a sensorial cortex, with different
input characteristics, in presence of transmission delays. We propose a new
measure to characterize collective behavior, based on the nonlinear extension
of the concept of Granger causality, and an interpretation is given of the
variation of the percentage of the causally relevant interactions with
transmission delays.Comment: 7 pages, 3 figures. To appear in the AIP seminar notes of 9th Granada
seminar on Computational Physics: Computational and Mathematical Modeling of
Cooperative Behavior in Neural System
Membrane Systems and Petri Net Synthesis
Automated synthesis from behavioural specifications is an attractive and
powerful way of constructing concurrent systems. Here we focus on the problem
of synthesising a membrane system from a behavioural specification given in the
form of a transition system which specifies the desired state space of the
system to be constructed. We demonstrate how a Petri net solution to this
problem, based on the notion of region of a transition system, yields a method
of automated synthesis of membrane systems from state spaces.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347
Flux Analysis in Process Models via Causality
We present an approach for flux analysis in process algebra models of
biological systems. We perceive flux as the flow of resources in stochastic
simulations. We resort to an established correspondence between event
structures, a broadly recognised model of concurrency, and state transitions of
process models, seen as Petri nets. We show that we can this way extract the
causal resource dependencies in simulations between individual state
transitions as partial orders of events. We propose transformations on the
partial orders that provide means for further analysis, and introduce a
software tool, which implements these ideas. By means of an example of a
published model of the Rho GTP-binding proteins, we argue that this approach
can provide the substitute for flux analysis techniques on ordinary
differential equation models within the stochastic setting of process algebras
Insights into the Second Law of Thermodynamics from Anisotropic Gas-Surface Interactions
Thermodynamic implications of anisotropic gas-surface interactions in a
closed molecular flow cavity are examined. Anisotropy at the microscopic scale,
such as might be caused by reduced-dimensionality surfaces, is shown to lead to
reversibility at the macroscopic scale. The possibility of a self-sustaining
nonequilibrium stationary state induced by surface anisotropy is demonstrated
that simultaneously satisfies flux balance, conservation of momentum, and
conservation of energy. Conversely, it is also shown that the second law of
thermodynamics prohibits anisotropic gas-surface interactions in "equilibrium",
even for reduced dimensionality surfaces. This is particularly startling
because reduced dimensionality surfaces are known to exhibit a plethora of
anisotropic properties. That gas-surface interactions would be excluded from
these anisotropic properties is completely counterintuitive from a causality
perspective. These results provide intriguing insights into the second law of
thermodynamics and its relation to gas-surface interaction physics.Comment: 28 pages, 11 figure
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