Ecological Modelling with the Calculus of Wrapped Compartments

The Calculus of Wrapped Compartments is a framework based on stochastic multiset rewriting in a compartmentalised setting originally developed for the modelling and analysis of biological interactions. In this paper, we propose to use this calculus for the description of ecological systems and we provide the modelling guidelines to encode within the calculus some of the main interactions leading ecosystems evolution. As a case study, we model the distribution of height of Croton wagneri, a shrub constituting the endemic predominant species of the dry ecosystem in southern Ecuador. In particular, we consider the plant at different altitude gradients (i.e. at different temperature conditions), to study how it adapts under the effects of global climate change.Comment: A preliminary version of this paper has been presented in CMC13 (LNCS 7762, pp 358-377, 2013

Rewriting Systems and the Modelling of Biological Systems

This paper gives a brief survey of the use of algebraic rewriting systems for modelling and simulating various biological processes, particularly at the cellular level

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

Membrane Computing as a Modeling Framework. Cellular Systems Case Studies

Membrane computing is a branch of natural computing aiming to abstract computing models from the structure and functioning of the living cell, and from the way cells cooperate in tissues, organs, or other populations of cells. This research area developed very fast, both at the theoretical level and in what concerns the applications. After a very short description of the domain, we mention here the main areas where membrane computing was used as a framework for devising models (biology and bio-medicine, linguistics, economics, computer science, etc.), then we discuss in a certain detail the possibility of using membrane computing as a high level computational modeling framework for addressing structural and dynamical aspects of cellular systems. We close with a comprehensive bibliography of membrane computing applications

Parallel Graph Rewriting Systems

In this paper we introduce a new theoretical paradigm, called PGR systems, which can be used to model in a discrete manner some natural phenomena occurring in-vivo/in-vitro en- vironments. PGR systems make use of graphs to describe the spatial structure of space of individuals, while the system dynamics caused by the movement/interaction of individuals is captured by the parallel applications of some graph rewriting rules. In this frame, an il- lustrative example is studied and based on it, an eloquent comparison between the abstract rewriting machines and PGR systems is done. Several further ideas to overcome the global computational effort needed for simulations, but still maintaining the overall ability for mod- eling are finally proposed

A Hybrid Approach to Modeling Biological Systems

This paper investigates a hybrid approach to modeling molecular interactions in biology. P systems, π-calculus, and Petri nets models, and two tools, Daikon, used in software reverse-engineering, and PRISM, a probabilistic model checker, are investigated for their expressiveness and complementary roles in describing and analyzing biological systems. A simple case study illustrates this approach

Drip and Mate Operations Acting in Test Tube Systems and Tissue-like P systems

The operations drip and mate considered in (mem)brane computing resemble the operations cut and recombination well known from DNA computing. We here consider sets of vesicles with multisets of objects on their outside membrane interacting by drip and mate in two different setups: in test tube systems, the vesicles may pass from one tube to another one provided they fulfill specific constraints; in tissue-like P systems, the vesicles are immediately passed to specified cells after having undergone a drip or mate operation. In both variants, computational completeness can be obtained, yet with different constraints for the drip and mate operations

Membrane systems with limited parallelism

Membrane computing is an emerging research field that belongs to the more general area of molecular computing, which deals with computational models inspired from bio-molecular processes. Membrane computing aims at defining models, called membrane systems or P systems, which abstract the functioning and structure of the cell. A membrane system consists of a hierarchical arrangement of membranes delimiting regions, which represent various compartments of a cell, and with each region containing bio-chemical elements of various types and having associated evolution rules, which represent bio-chemical processes taking place inside the cell. This work is a continuation of the investigations aiming to bridge membrane computing (where in a compartmental cell-like structure the chemicals to evolve are placed in compartments defined by membranes) and brane calculi (where one considers again a compartmental cell-like structure with the chemicals/proteins placed on the membranes themselves). We use objects both in compartments and on membranes (the latter are called proteins), with the objects from membranes evolving under the control of the proteins. Several possibilities are considered (objects only moved across membranes or also changed during this operation, with the proteins only assisting the move/change or also changing themselves). Somewhat expected, computational universality is obtained for several combinations of such possibilities. We also present a method for solving the NP-complete SAT problem using P systems with proteins on membranes. The SAT problem is solved in O(nm) time, where n is the number of boolean variables and m is the number of clauses for an instance written in conjunctive normal form. Thus, we can say that the solution for each given instance is obtained in linear time. We succeeded in solving SAT by a uniform construction of a deterministic P system which uses rules involving objects in regions, proteins on membranes, and membrane division. Then, we investigate the computational power of P systems with proteins on membranes in some particular cases: when only one protein is placed on a membrane, when the systems have a minimal number of rules, when the computation evolves in accepting or computing mode, etc. This dissertation introduces also another new variant of membrane systems that uses context-free rewriting rules for the evolution of objects placed inside compartments of a cell, and symport rules for communication between membranes. The strings circulate across membranes depending on their membership to regular languages given by means of regular expressions. We prove that these rewriting-symport P systems generate all recursively enumerable languages. We investigate the computational power of these newly introduced P systems for three particular forms of the regular expressions that are used by the symport rules. A characterization of ET0L languages is obtained in this context