A Study of the Robustness of the EGFR Signalling Cascade Using Continuous Membrane Systems

Many approaches to anticancer treatment have had a limited success. A fundamental hurdle to cancer therapy is the robustness of the signalling networks involved in tumourgenesis. The complexity of net- works of biological signalling pathways is such that the development of simplifying models is essential in trying to understand the wide-ranging cellular responses they can generate. In this paper a model of the epider- mal growth factor receptor signalling cascade is developed using contin- uous membrane systems. This model is used to study the robustness of this signalling cascade which is known to play a key role in tumour cell proliferation, angiogenesis and metastasis.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

A CLIPS Simulator for Recognizer P Systems with Active Membranes

In this paper we propose a new way to represent recognizer P systems with active membranes based on Production Systems techniques. This representation allows us to express the set of rules and the configurations in each step of the evolution as facts in a knowledge base. We provide a CLIPS program to simulate the evolutions of this variant of P systems.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

Modelling gene expression control using P systems: The Lac Operon, a case study

In this paper P systems are used as a formal framework for the specification and simulation of biological systems. In particular, we will deal with gene regulation systems consisting of protein–protein and protein–DNA interactions that take place in different compartments of the hierarchical structure of the living cell or in different individual cells from a colony. We will explicitly model transcription and translation as concurrent and discrete processes using rewriting rules on multisets of objects and strings. Our approach takes into account the discrete character of the components of the system, its random behaviour and the key role played by membranes in processes involving signalling at the cell surface and selective uptake of substances from the environment. Our systems will evolve according to an extension of Gillespie’s algorithm, called Multicompartmental Gillespie’s Algorithm. The well known gene regulation system in the Lac Operon in Escherichia coli will be modelled as a case study to benchmark our approach.Ministerio de Ciencia y Tecnología TIN2005-09345-C04-0

Trading Polarization for Bi-stable Catalysts in P Systems with Active Membranes

In the last time, several efforts have been made in order to remove polarizations of membranes from P systems with active membranes; the present paper is a contribution in this respect. In order to compensate the loss of power represented by avoiding polarizations, we use bi-stable catalysts. Polarizationless systems with active membranes which use bi-stable catalysts are proven to be computationally complete and able to solve efficiently NP-complete problems. In this paper we present a solution to SAT in linear time. In order to illustrate the presented solution, we also provide a simulation with CLIPS.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

Solving the BINPACKING Problem by Recognizer P Systems with Active Membranes

In this paper we present an e®ective solution to the BINPACKING problem using a family of recognizer P systems with active membranes, input membrane and external output. The analysis of the solution presented here will be done form the point of view of complexity classes.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-

Modelling EGFR signalling cascade using continuous membrane systems

The complexity of networks of biological signalling pathways is such that the development of simplifying models is essential in trying to understand the wide-ranging cellular responses they can generate. In this paper a continuous variant of membrane systems is introduced and used to model the epidermal growth factor receptor signalling network which is known to play a key role in tumour cell proliferation, angiogenesis and metastasis.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

A Model of the Quorum Sensing System in Vibrio fischeri Using P Systems

Quorum sensing is a cell density dependent gene regulation system that allows an entire population of bacterial cells to communicate in order to regulate the expression of certain or specific genes in a coordinated way depending on the size of the population. In this paper we present a model of the Quorum Sensing System in Vibrio fischeri using a variant of membrane systems called P systems. In this framework each bacterium and the environment are represented by membranes and the rules are applied according to an extension of Gillespie’s Algorithm called Multicompartmental Gillespie’s Algorithm. This algorithm runs on more than one compartment and takes into account the disturbance produced when chemical substances diffuse from one compartment or region to another. Our approach allows us to examine the individual behaviour of each bacterium as an agent as well as the emergent behaviour of the colony as a whole and the processes of swarming and recruitment. Our simulations show that at low cell densities bacteria remain dark while at high cell densities some bacteria start to produce light and a recruitment process takes place that makes the whole colony of bacteria to emit light. Our computational modelling of quorum sensing could provide insights that may enable researchers to develop new applications where multiple agents need to robustly and efficiently coordinate their collective behaviour based only on a very limited information of the local environment

Attacking the Common Algorithmic Problem by Recognizer P Systems

Many NP-complete problems can be viewed as special cases of the Common Algorithmic Problem (CAP). In a precise sense, which will be defined in the paper, one may say that CAP has a property of local universality. In this paper we present an effective solution to the decision version of the CAP using a family of recognizer P systems with active membranes. The analysis of the solution presented here will be done from the point of view of complexity classes in P systems.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

Modelling Vibrio fischeri’s behaviour Using P Systems

Quorum sensing is a cell density dependent gene regulation system that allows an entire population of bacterial cells to communicate in order to regulate the expression of certain or specific genes in a coordinated way depending on the size of the population. In this paper we present a model of the Quorum Sensing System in Vibrio fischeri using a variant of membrane systems called P systems. In this framework each bacterium and the environment are represented by membranes and the rules are applied according to probabilities computed using mass action law. This approach allows us to examine the individual behaviour of each bacterium as an agent as well as the behaviour of the colony as a whole and the processes of swarming and recruitment. Our simulations show that at low cell densities the bacteria remain dark while at high cell densities some bacteria start to produce light and a recruitment process takes place that makes the whole colony of bacteria to emit light. The above mentioned behaviour of our in silico bacteria maps well experiments and in vitro observations.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0