Book ChapterDOI
Brane calculi
Luca Cardelli
- pp 257-278
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This work introduces a family of process calculi with dynamic nested membranes that are tightly coupled to membranes, and can perform interactions on both sides of a membrane.Abstract:
We introduce a family of process calculi with dynamic nested membranes. In contrast to related calculi, including some developed for biological applications, active entities here are tightly coupled to membranes, and can perform interactions on both sides of a membrane. That is, computation happens on the membrane, not inside of it.read more
Citations
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Journal ArticleDOI
Formal molecular biology
Vincent Danos,Cosimo Laneve +1 more
TL;DR: A finer-grained concurrent model, the mK-calculus, is considered, where interactions have to be at most binary, and it is shown how to embed the coarser- grained language in the latter, a properly which the authors call self-assembly.
Rule-based modelling of cellular signalling
TL;DR: In this paper, the authors adapt the notions of causality and conflict, familiar from concurrency theory, to?, their representation language of choice, and show how causality enables the formalization of the colloquial concept of pathway and, perhaps more surprisingly, how conflict can be used to dissect the signalling dynamics to obtain a qualitative handle on the range of system behaviours.
Book ChapterDOI
Rule-based modelling of cellular signalling
TL;DR: It is shown how causality enables the formalization of the colloquial concept of pathway and, perhaps more surprisingly, how conflict can be used to dissect the signalling dynamics to obtain a qualitative handle on the range of system behaviours.
Book ChapterDOI
Scalable simulation of cellular signaling networks
TL;DR: A radically different method which does not attempt to count species is presented, which uses a representation of the system together with a super-approximation of its 'event horizon' (all events that may happen next), and a specific correction scheme to obtain exact timings.
Journal ArticleDOI
Modeling and querying biomolecular interaction networks
TL;DR: This work proposes to use the computation tree logic (CTL) as a query language for querying the possible behaviors of the system and illustrates the expressivity of this language by proposing a formal counterpart of Kohn's compilation on the mammalian cell-cycle control.
References
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Journal ArticleDOI
From molecular to modular cell biology.
TL;DR: General principles that govern the structure and behaviour of modules may be discovered with help from synthetic sciences such as engineering and computer science, from stronger interactions between experiment and theory in cell biology, and from an appreciation of evolutionary constraints.
Book
Communicating and Mobile Systems: the Pi-Calculus
TL;DR: Communicating Systems: Behaviour of automata and Observation equivalence: theory, examples, and Discussion and related work Bibliography Index.
Journal ArticleDOI
Mobile ambients
Luca Cardelli,Andrew D. Gordon +1 more
TL;DR: In this article, a calculus describing the movement of processes and devices, including movement through administrative domains, is introduced, which is similar to the one we use in this paper. But it is different from ours.
Journal ArticleDOI
It’s a noisy business! Genetic regulation at the nanomolar scale
Harley H. McAdams,Adam P. Arkin +1 more
TL;DR: Many molecules that control genetic regulatory circuits act at extremely low intracellular concentrations, which causes large random variation in rates of development, morphology and the instantaneous concentration of each molecular species in each cell.
Journal ArticleDOI
Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems
TL;DR: The map shows how multiprotein complexes could assemble and function at gene promoter sites and at sites of DNA damage and portrays the richness of connections between the p53-Mdm2 subsystem and other parts of the network.