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Article
Open AccessCharacterization and computation of ancestors in reaction systems
In reaction systems, preimages and nth ancestors are sets of reactants leading to the production of a target set of products in either 1 or n steps, respectively. Many computational problems on preimages and ance...
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Article
Open AccessA survey of gene regulatory networks modelling methods: from differential equations, to Boolean and qualitative bioinspired models
Gene Regulatory Networks (GRNs) represent the interactions among genes regulating the activation of specific cell functionalities, such as reception of (chemical) signals or reaction to environmental changes. ...
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Article
Generalized contexts for reaction systems: definition and study of dynamic causalities
Reaction systems are a qualitative formalism for the modelling of systems of biochemical reactions. In their original formulation, a reaction system executes in an environment (or context) that c...
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Chapter and Conference Paper
Multiset Patterns and Their Application to Dynamic Causalities in Membrane Systems
In this paper we investigate dynamic causalities in membrane systems by proposing the concept of “predictor”, originally defined in the context of Ehrenfeucht and Rozemberg’s reaction systems. The goal is to c...
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Chapter and Conference Paper
Computing Preimages and Ancestors in Reaction Systems
In reaction systems, preimages and n-th ancestors are sets of reactants leading to the production of a target set of products in either one or n steps, respectively. Many computational problems on preimages and a...
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Chapter and Conference Paper
Applications of P Systems in Population Biology and Ecology: The Cases of MPP and APP Systems
We describe two extensions of P systems for the modelling of populations and ecosystems. They are the Minimal Probabilistic P systems (MPP systems) and the Attributed Probabilistic P systems (APP systems). We ...
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Chapter and Conference Paper
A Mathematical Model for Assessing KRAS Mutation Effect on Monoclonal Antibody Treatment of Colorectal Cancer
The most challenging task in colorectal cancer research nowadays is to understand the development of acquired resistance to anti-EGFR drugs. The key reason for this problem is the KRAS mutations produced after...
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Chapter and Conference Paper
Attributed Probabilistic P Systems and Their Application to the Modelling of Social Interactions in Primates
We propose a variant of probabilistic P Systems, Attributed Probabilistic P systems (APP systems), in which objects are annotated with attributes. We use APP systems for modelling social behaviours of some spe...
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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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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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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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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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Article
Open AccessFine-tuning anti-tumor immunotherapies via stochastic simulations
Anti-tumor therapies aim at reducing to zero the number of tumor cells in a host within their end or, at least, aim at leaving the patient with a sufficiently small number of tumor cells so that the residual t...
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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
Foreword
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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 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...
