Causal static analysis for Brane Calculi

We present here a static analysis, based on Abstract Interpretation, obtained by defining an abstract version of the causal semantics for the Mate/Bud/Drip (MBD) version of Brane Calculi, proposed by Busi. Our analysis statically approximates the dynamic behaviour of MBD systems. More precisely, the analysis is able to describe the essential behaviour of the represented membranes, in terms of their possible interactions. Furthermore, our analysis is able to statically capture the possible causal dependencies among interactions, whose determination can be exploited to better understand the modelled biological phenomena. Finally, we apply our analysis to an abstract specification of the receptor-mediated endocytosis mechanism

A static analysis for Brane Calculi providing global occurrence counting information

In this paper we propose a static analysis for Brane Calculi [1], based on Abstract Interpretation [2] techniques. Our analysis statically approximates the dynamic behaviour of Brane systems, by providing a description of the possible hierarchical structure of membranes and of the processes possibly associated to each membrane, together with global occurrence counting information. Our analysis can be computed in polynomial time. We apply it to investigate several biological systems in which occurrence counting information plays a crucial role. In particular, our case study concerns the formation of the haemoglobin polymer in presence of alterations and investigate the influence that such alterations have on the ability of the haemoglobin polymer to bind oxygen molecules

Modelling Biological Systems From Molecular Interactions to Population Dynamics

Biological systems are examples of complex systems, which consist of several interacting components. Understanding the behaviour of such systems requires a multidisciplinary approach that encompasses biology, mathematics, computer science, physiscs and chemistry. New research areas are emerging as the result of this multidisciplinarity, such as bioinformatics, systems biology and computational biology. Computer science plays an important role in the newly emerging research areas by offerring techniques, algorithms, languages and software to solve research problems efficiently. On the other hand, the efforts to solve these research problems stimulate the development of new and better computer science techniques, algorithms, languages and software. This thesis describes our approach in modelling biological systems as a way to better understand their complex behaviours. Our approach is based on the Calculi of Looping Sequences, a class of formalisms originally developed to model biological systems involving cells and their membrane-based structures. We choose Stochastic CLS and Spatial CLS, two variants of the calculi that support quantitative analysis of the model, and define an approach that support simulation, statistical model-checking and visualisation as analysis techniques. Moreover, we found out that this class of formalisms can be easily extended to model population dynamics of animals, a kind of biological systems that does not involve membrane-based structures