Behavioural observations of cell movements with timing aspects

Theoretical Computer Science, 2007

Existing results in membrane computing refer mainly to P systems’ characterization of Turing computability, also to some polynomial solutions to NP-complete problems by using an exponential workspace created in a “biological way”. In this paper we define an operational semantics of a basic class of P systems, and give two implementations of the operational semantics using rewriting logic. We present some results regarding these implementations, including two operational correspondence results, and discuss why these implementations are relevant in order to take advantage of good features of both structural operational semantics and rewriting logic.

Lecture Notes in Computer Science, 2014

Cellular automata are discrete mathematical models that have been proven useful as representations of a wide variety of systems exhibiting emergent behavior. Detection of emergent behavior is typically computationally expensive as it relies on computer simulations. We propose to specify cellular automata using a suitable Temporal Description Logic and we show that we can formulate queries about the evolution of a cellular automaton as reasoning tasks in this logic.

Theoretical Computer Science, 2016

The behavior of biochemical systems such as metabolic and signaling pathways may depend on either the location of the reactants or on the time needed for a reaction to occur. In this paper we propose a formalism for specifying and verifying properties of biochemical systems that combines, coherently, temporal and spatial modalities. To this aim, we consider a fragment of intuitionistic linear logic with subexponentials (SELL). The subexponential signature allows us to capture the spatial relations among the different components of the system and the timed constraints. We illustrate our approach by specifying some well-known biological systems and verifying properties of them. Moreover, we show that our framework is general enough to give a logic-based semantics to P systems. We show that the proposed logical characterizations have a strong level of adequacy. Hence, derivations in SELL follow exactly the behavior of the modeled system.

Electronic Notes in Theoretical Computer Science, 2015

Biochemical systems such as metabolic and signaling pathways tend to be arranged in a physical space: the product of one reaction must be in the right place to become the reactant for the subsequent reaction in the pathway. Moreover, in some cases, the behavior of the systems can depend on both, the location of the reactants as well as on the time needed for the reaction to occur. We address the problem of specifying and verifying properties of biochemical systems that exhibit both temporal and spatial modalities at the same time. For that, we use as specification language a fragment of intuitionistic linear logic with subexponentials (SELL). The subexponential signature allows us to capture the spatial relations among the different components of the system and the timed constraints for reactions to occur. We show that our framework is general enough to give a declarative semantics to P-Systems and we show that such logical characterization has a strong level of adequacy. Hence, derivations in SELL follow exactly the behavior of the modeled system.

2005

In this paper we discuss several representation issues that we came across while modelling molecular interactions in cells of living organisms. One of the issues was that the triggering of events inside cells, an important modelling component, are not necessarily immediate, leading to multiple evolution models in the absence of additional information. Second, often an action or a trigger at one level of granularity of representation can be elaborated and refined. We show the problem that existing representation and modelling formalisms have in dealing with the above issues. We then present an action language which builds up on a previous language, and has the ability to express event ordering knowledge. We show that our language is able to adequately address the above-mentioned issues.

Arxiv preprint arXiv:1108.0496, 2011

Membrane computing is a well-established and successful research field which belongs to the more general area of molecular computing. Membrane computing aims at defining parallel and non-deterministic computing models, called membrane systems or P Systems, which abstract from the functioning and structure of the cell. A membrane system consists of a spatial structure, a hierarchy of membranes which do not intersect, with a distinguishable membrane called skin surrounding all of them. A membrane without any other membranes inside is elementary, while a nonelementary membrane is a composite membrane. The membranes define demarcations between regions; for each membrane there is a unique associated region. Since we have a one-to-one correspondence, we sometimes use membrane instead of region, and vice-versa. The space outside the skin membrane is called the environment.

International Journal of Computer Mathematics, 2013

This article introduces a general formalism/framework flexible enough to cover descriptions of different variants of P systems having a dynamic membrane structure. Our framework can be useful for the precise definition of new variants of P systems with a dynamic structure and for the comparison of existing definitions as well as for their extension. We give a detailed definition of the formalism and we present some examples of how to translate several existing variants of P systems with a dynamic structure.

In this paper we introduce mutual mobile membranes with surface objects, systems which have biological motivation. In P systems with mobile membranes with surface objects, a membrane may enter or exit another membrane. The second membrane just undergoes the action, meaning that it has no control on when the movement takes place. This kind of movement illustrates the lack of an agreement (synchronization) similar to an asynchronous evolution. In mutual mobile membranes with surface objects this aspect is adjusted: any movement takes place only if both participants agree by synchronizing their evolution. In membranes two kinds of competition can occur: resource competition and location competition. Resource competition refers to rules which request the same resources, and the available resources can only be allocated to some of the rules. Location competition refers to the movement of a membrane in the hierarchical structure of the membrane systems under the request of some conflict rules. We use the two variants of membrane systems in order to describe and explain these kinds of competition, and introduce synchronizing objects in mutual mobile membranes which will help to solve the resource and location competitions.

2006

Logics for expressing properties of Petri hypernets, a visual formalism for modelling mobile agents, are proposed. Two classes of properties are of interest-the temporal evolution of agents and their structural correlation. In particular, we investigate how the classes can be combined into a logic capable of expressing the dynamic evolution of the structural correlation. The problem of model checking properties of a class of the logic on Petri hypernets is shown to be PSPACE-complete.

Natural Computing, 2011

In this paper we introduce mutual mobile membranes with surface objects, systems which have biological motivation. In P systems with mobile membranes with surface objects, a membrane may enter or exit another membrane. The second membrane just undergoes the action, meaning that it has no control on when the movement takes place. This kind of movement illustrates the lack of an agreement (synchronization) similar to an asynchronous evolution. In mutual mobile membranes with surface objects this aspect is adjusted: any movement takes place only if both participants agree by synchronizing their evolution. In membranes two kinds of competition can occur: resource competition and location competition. Resource competition refers to rules which request the same resources, and the available resources can only be allocated to some of the rules. Location competition refers to the movement of a membrane in the hierarchical structure of the membrane systems under the request of some conflict rules. We use the two variants of membrane systems in order to describe and explain these kinds of competition, and introduce synchronizing objects in mutual mobile membranes which will help to solve the resource and location competitions.