1,283 research outputs found
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
Dependencies and Simultaneity in Membrane Systems
Membrane system computations proceed in a synchronous fashion: at each step
all the applicable rules are actually applied. Hence each step depends on the
previous one. This coarse view can be refined by looking at the dependencies
among rule occurrences, by recording, for an object, which was the a rule that
produced it and subsequently (in a later step), which was the a rule that
consumed it. In this paper we propose a way to look also at the other main
ingredient in membrane system computations, namely the simultaneity in the rule
applications. This is achieved using zero-safe nets that allows to synchronize
transitions, i.e., rule occurrences. Zero-safe nets can be unfolded into
occurrence nets in a classical way, and to this unfolding an event structure
can be associated. The capability of capturing simultaneity of zero-safe nets
is transferred on the level of event structure by adding a way to express which
events occur simultaneously
Researching Framework for Simulating/Implementating P Systems
Researching simulation/implementation of membranes systems is very recent. Present literature
gathers new publications frequently about software/hardware, data structures and algorithms for implementing P
system evolution.
In this context, this work presents a framework which goal is to make tasks of researchers of this field easier.
Hence, it establishes the set of cooperating classes that form a reusable and flexible design for the customizable
evaluation with new data structures and algorithms. Moreover, it includes customizable services for correcting,
monitoring and logging the evolution and edition, recovering, automatic generating, persistence and visualizing P
systems
Modelling of Multi-Agent Systems: Experiences with Membrane Computing and Future Challenges
Formal modelling of Multi-Agent Systems (MAS) is a challenging task due to
high complexity, interaction, parallelism and continuous change of roles and
organisation between agents. In this paper we record our research experience on
formal modelling of MAS. We review our research throughout the last decade, by
describing the problems we have encountered and the decisions we have made
towards resolving them and providing solutions. Much of this work involved
membrane computing and classes of P Systems, such as Tissue and Population P
Systems, targeted to the modelling of MAS whose dynamic structure is a
prominent characteristic. More particularly, social insects (such as colonies
of ants, bees, etc.), biology inspired swarms and systems with emergent
behaviour are indicative examples for which we developed formal MAS models.
Here, we aim to review our work and disseminate our findings to fellow
researchers who might face similar challenges and, furthermore, to discuss
important issues for advancing research on the application of membrane
computing in MAS modelling.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314
P Colony Automata with LL(k)-like Conditions
We investigate the possibility of the deterministic parsing (that is, parsing
without backtracking) of languages characterized by (generalized) P colony automata.
We de ne a class of P colony automata satisfying a property which resembles the LL(k)
property of context-free grammars, and study the possibility of parsing the characterized
languages using a k symbol lookahead, as in the LL(k) parsing method for context-free
languages
No Cycles in Compartments. Starting from Conformon-P Systems
Starting from proofs of results about the computing power of conformon-
P systems, we infer several results about the power of certain classes of tissue-like P
systems with (cooperative) rewriting rules used in an asynchronous way, without cycles
in compartments. This last feature is related to an important restriction appearing when
dealing with lab implementations of P systems, that of avoiding local evolution loops of
objects
Generalized Communicating P Systems Working in Fair Sequential Model
In this article we consider a new derivation mode for generalized
communicating P systems (GCPS) corresponding to the functioning of population
protocols (PP) and based on the sequential derivation mode and a fairness
condition. We show that PP can be seen as a particular variant of GCPS. We also
consider a particular stochastic evolution satisfying the fairness condition
and obtain that it corresponds to the run of a Gillespie's SSA. This permits to
further describe the dynamics of GCPS by a system of ODEs when the population
size goes to the infinity.Comment: Presented at MeCBIC 201
Impact of Membrane Computing and P Systems in ISI WoS. Celebrating the 65th Birthday of Gheorghe Păun
Membrane Computing is a branch of Computer Science initiated by Gheorghe Păun in 1998, in a technical report of Turku Centre for Computer Science published as a journal paper ("Computing with Membranes" in Journal of Computer and System Sciences) in 2000. Membrane systems, as Gheorghe Păun called the models he has introduced, are known nowadays as "P Systems" (with the letter P coming from the initial of the name of this research area "father"). This note is an overview of the impact in ISI WoS of Gheorghe Păun’s works, focused on Membrane Computing and P Systems field, on the occasion of his 65th birthday anniversary
On Modeling Signal Transduction Networks
Signal transduction networks are very complex processes employed by the
living cell to suitably react to environmental stimuli. Qualitative and quantitative computational
models play an increasingly important role in the representation of these
networks and in the search of new insights about these phenomena. In this work we analyze
some graph-based models used to discover qualitative properties of such networks.
In turn, we show that MP systems can naturally extend these graph-based models by
adding some qualitative elements. The case study of integrins activation during the lymphocyte
recruitment, a crucial phenomenon in inflammatory processes, is described, and
a first MP graph for this network is designed. Finally, we discuss some open problems
related to the qualitative modeling of signaling networks
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