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Chapter and Conference Paper
Modeling Long–Running Transactions with Communicating Hierarchical Timed Automata
Long-running transactions consist of tasks which may be executed sequentially and in parallel, may contain sub-tasks, and may require to be completed before a deadline. These transactions are not atomic and, i...
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Chapter and Conference Paper
Bisimulation Congruences in the Calculus of Loo** Sequences
The Calculus of Loo** Sequences (CLS) is a calculus suitable to describe biological systems and their evolution. CLS terms are constructed by starting from basic constituents and composing them by means of o...
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Chapter and Conference Paper
Extending the Calculus of Loo** Sequences to Model Protein Interaction at the Domain Level
In previous papers we introduced a formalism, called Calculus of Loo** Sequences (CLS), for describing biological systems and their evolution. CLS is based on term rewriting. Terms can be constructed by comp...
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Chapter and Conference Paper
The Calculus of Loo** Sequences for Modeling Biological Membranes
We survey the formalism Calculus of Loo** Sequences (CLS) and a number of its variants from the point of view of their use for describing biological membranes. The CLS formalism is based on term rewriting an...
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Chapter and Conference Paper
Stochastic Calculus of Loo** Sequences for the Modelling and Simulation of Cellular Pathways
The paper presents the Stochastic Calculus of Loo** Sequences (SCLS) suitable to describe microbiological systems, such as cellular pathways, and their evolution. Systems are represented by terms. The terms ...
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Chapter and Conference Paper
The Calculus of Loo** Sequences
We describe the Calculus of Loo** Sequences (CLS) which is suitable for modeling microbiological systems and their evolution. We present two extensions, CLS with links (LCLS) and Stochastic CLS. LCLS simplif...
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Article
Bisimulations in calculi modelling membranes
Bisimulations are well-established behavioural equivalences that are widely used to study properties of computer science systems. Bisimulations assume the behaviour of systems to be described as labelled trans...
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Chapter and Conference Paper
Probabilistic Model Checking of Biological Systems with Uncertain Kinetic Rates
We present an abstraction of the probabilistic semantics of Multiset Rewriting to formally express systems of reactions with uncertain kinetic rates. This allows biological systems modelling when the exact rat...
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Chapter and Conference Paper
Simulation of Kohn’s Molecular Interaction Maps through Translation into Stochastic CLS+
Kohn’s Molecular Interaction Maps (MIMs) are a graphical notation for describing bioregulatory networks at the molecular level. Even if the meaning of Kohn’s diagrams can be often easily understood, in many ca...
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Chapter and Conference Paper
Membrane Systems Working in Generating and Accepting Modes: Expressiveness and Encodings
Membrane systems can be seen either as generators or as acceptors of multiset languages. In this paper we compare the expressive power of membrane systems working in accepting mode with that of membrane system...
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Chapter
Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach
Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed. Mathematical modeling of biological systems with delays is usually based on Delay Differ...
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Article
Spatial P systems
We present Spatial P systems, a variant of P systems which embodies the concept of space and position inside a membrane. Objects in membranes are associated with positions. Rules specify, in the usual way, the...
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Chapter
Modelling Biochemical Pathways with the Calculus of Loo** Sequences
The Calculus of Loo** Sequences (CLS) has been proposed as a formalism for representing and simulating biomolecular systems. CLS is based on a set of operators which allow to represent the structure of such ...
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Article
Open AccessPopulation dynamics with a mixed type of sexual and asexual reproduction in a fluctuating environment
Carassius gibelio, a cyprinid fish from Eurasia, has the ability to reproduce both sexually and asexually. This fish is also known as an invasive species which colonized almost all continental Europe, most likely...
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Chapter and Conference Paper
A Compositional Semantics of Reaction Systems with Restriction
Reaction systems are an abstract model of interactions among biochemical reactions, developed around two opposite mechanisms: facilitation and inhibition. The evolution of a Reaction System is driven by the ex...
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Chapter and Conference Paper
Modelling Population Dynamics Using Grid Systems
A new formalism, Grid Systems, aimed at modelling population dynamics is presented. The formalism is inspired by concepts of Membrane Computing (P Systems) and spatiality dynamics of Cellular Automata. The semant...
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Chapter and Conference Paper
A Computational Formal Model of the Invasiveness of Eastern Species in European Water Frog Populations
European water frog populations are mainly composed by two species: Pelophylax lessonae (pool frog) and Pelophylax esculentus (edible frog). These populations are called L-E complexes. Edible frogs are a hybrid f...
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Chapter
Systolic Automata and P Systems
Systolic automata are models of highly-concurrent language acceptors based on identical processors with one-way flow of information, amenable to efficient hardware implementation as multiprocessor chips.
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Article
Open AccessThe role of deleterious mutations in the stability of hybridogenetic water frog complexes
Some species of water frogs originated from hybridization between different species. Such hybrid populations have a particular reproduction system called hybridogenesis. In this paper we consider the two species
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Article
Identification of components in biochemical pathways: extensive application to SBML models
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity, such as a protein, in all its states (...
