Membrane Computing

Name: Membrane Computing | 12th International Conference, CMC 2011, Fontainebleau, France, August 23-26, 2011, Revised Selected Papers
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12th International Conference, CMC 2011, Fontainebleau, France, August 23-26, 2011, Revised Selected Papers

Marian Gheorghe Gheorghe Paun Grzegorz Rozenberg Arto Salomaa Sergey Verlan(Herausgeber*in)

Springer (Verlag)

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Erschienen am 13. Januar 2012

380 Seiten

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Inhalt

Title Page
Preface
Table of Contents
Invited Presentations
Properties of Membrane Systems
Introduction
Dynamic Properties
Effect of Determinism
Other Models Where Non-determinism Seems Essential
Effect of Other Variants of Determinism, Reversibility, Confluence and Similar Properties
Effect of Other Properties
Self-stabilization
Conclusions
References
Bridging Biology and Engineering Together with Spatial Computing
Motivation
Space as a Unifying Abstraction
Example Applications
Future Directions
References
The Modeling and the Simulation of the Fluid Machines of Synthetic Biology
Introduction
A Brief Introduction to MGS
Lessons from L Systems and P Systems
The Topological Organization of the State
Topological Rewriting
The Modeling of a ``Multicellular Bacteria''
The international Genetically Engineered Machine (iGEM) Competition
Objectives of the Synthetic Multicellular Bacterium Project
The Paris Team Proposal
One MGS Model of the Synthetic Multicellular Bacterium
Conclusions
References
Parallel and Distributed Algorithms in P Systems
Introduction
Preliminaries-Basic Model
Extensions-P Modules
Extension-Complex Symbols
Extension-Generic Rules
Extension-Cell IDs
Asynchronous P Systems
Discovering Neighbours (Async)
Echo Algorithm (Async)
Parallel Stereo Matching
Conclusions
References
Variants of Distributed P Automata and the Efficient Parallelizability of Languages
Introduction
Preliminaries and Definitions
The Power of P Automata and the Influence of the Input Mapping
Distributed P Automata and the Parallelizability of Languages
The Linear Speedup of P Automata and the Efficiency of Parallelization
Efficient Parallelizability with More Than a Constant Amount of Inter-component Communication
Conclusions and Further Suggestions for Research
References
Regular Presentations
Quantitative Causality in Membrane Systems
Introduction
Multisets in Membrane Systems
Specific and General Causality
Quantitative Results
Conclusion and Related Work
References
Circular Post Machines and P Systems with Exo-insertion and Deletion
Introduction
Preliminaries
Circular Post Machines
Insertion and Deletion
Distributed Insertion-Deletion
Results
A New Variant of Circular Post Machines
P Systems with Priority of Exo-deletion
One-Sided Insertion/Deletion without Priorities
Conclusions
References
A Spiking Neural P System Simulator Based on CUDA
Introduction
Spiking Neural P Systems
The SNP System Model
Examples of SNP Systems
Matrix Representation of SNP Systems
GPU Computing
Compute Unified Device Architecture (CUDA)
SNP System GPU Simulation Considerations
Simulating SNP Systems in CUDA
Simulation Results and Observations
Conclusions and Future Work
References
Modularity in P Colonies with Checking Rules
Introduction
Definitions
P Colonies
Register Machines
Modularity in the Terms of P Colonies
P Colonies with One Object Inside the Agent
Conclusion
References
Finite dP Automata versus Multi-head Finite Automata
Introduction
Preliminaries
One-Way Multi-head Finite Automata versus Finite dP Automata
Two-Way Multi-head Finite Automata versus Finite dP Automata
Further Remarks
References
An Adaptive Algorithm for P System Synchronization
Introduction
Preliminaries
Deterministic FSSP Solution for Rooted Trees
P Systems for Solving the FSSP for Rooted Trees
Phase I: Find the Middle Cell of Rooted Trees
Phase II: Determine the Step to Enter the Firing State
Empirical Work
FSSP Solution for Digraphs
P Systems for Solving the FSSP for Digraphs
Phase I: Find the Middle Cell of a BFS Spanning Tree
Phase II: Determine the Step to Enter the Firing State
Empirical Work
Conclusions and Future Works
References
P Systems with Active Membranes Operating under Minimal Parallelism
Introduction
Basic Definitions
Operational Modes in P Systems
Solving NP-Complete and PP-Complete Problems
Computational Power
Final Remarks
References
Chemical Analog Computers for Clock Frequency Control Based on P Modules
Introduction
P Modules
Chemical Analog Computer Components
Mass-Action Kinetics
Addition
Non-negative Subtraction
Multiplication
Division
Square Root
Low-Pass Filter
Integrator and Differentiator
Clock Frequency Control Using Phase-Locked Loops
A Controllable Goodwin-Type Core Oscillator
Goodwin-Type Circadian Clock Control by Phase-Locked Loop
Conclusions
References
Evolutionary Design of a Simple Membrane System
Introduction
Problem Description
Cell-Like P Systems
Problem Statement
Evolutionary Design
Experiments and Results
An Example for Computing n2
Comparison with Genetic Algorithms
Conclusions
References
Formal Verification of P Systems with Active Membranes through Model Checking
Introduction
Background
P Systems
Linear Temporal Logic
Theoretical Basis for Model Checking of P Systems with Active Membranes
Case Study: The Subset Sum Problem
Experimental Results
Related Work
Conclusions and Future Work
References
Basic Concurrency Resolution in Clock-Free P Systems
Introduction
Concurrency: Clock-Free P Systems vs. P Systems with a Global Clock
Preliminaries
P Systems
Concurrency
Strategies
Synchronisation of Rule Applications
Sequential Strategy
Barrier Synchronisation Strategy
Synchronisation of Processes
Lock
Semaphore
The Dining Philosophers Problem
Conclusion
References
Asynchronous Extended Spiking Neural P Systems with Astrocytes
Introduction
Prerequisites
Spiking Neural P Systems with Astrocytes
Universality of ASNPA Systems
Conclusions and Remarks
References
A P--Lingua Based Simulator for Spiking Neural P Systems
Introduction
Preliminaries
P-Lingua Syntax for SN P Systems
Regular Expressions
Model Specification
Sample of the First Few Lines of a P-Lingua SN P System Definition File
Definition of Multisets
Definition of Rules
Definition of the Output
Reserved Words
A Simulator Software for SN P Systems
An Example: A Family of SN P Systems Solving SAT
Description of the Family
A P-Lingua Source Code. Particular Instance Solution of SAT Problem
Generalized P-Lingua Source Code for the Family of SN P Systems Solving SAT
Simulation Results
Performance
Conclusions and Future Work
References
Computing with Multi-membranes
Introduction
Multi-membranes
Computing with Multi-membranes
Examples of Multi-membrane Systems
Computational Universality
More Complex Examples of Computation
Conclusions
References
A Methodology Based on MP Theory for Gene Expression Analysis
Introduction
Gene Networks
MP Modelling of Gene Networks
From Raw Data to MP Models
Normalization and Reduction of Raw Data
Data Filtering
Data Clustering
From Data Clustering to Gene Networks via MP Systems
Conclusions
References
Generalized Gandy-P\?aun-Rozenberg Machines for Tile Systems and Cellular Automata
Introduction
generalized Gandy-¶-Rozenberg Machines
generalized G-P-R Machines for Cellular Automata
Conclusion
Appendix
References
Sequentiality Induced by Spike Number in SNP Systems: Small Universal Machines
Introduction
Basic Description and Definitions
Spiking Neural P Systems
Max Pseudo-sequentiality Result
Final Remarks
References
P Systems Simulating Oracle Computations
Introduction
Definitions
Simulating Turing Machines
Simulating Oracle Machines
Informal Description of the Simulation of Oracle Queries
Technical Details
Main Result
Conclusions
References
P Systems with Chained Rules
Introduction
Preliminaries
Lindenmayer Systems
Register Machines
P Systems with Chained Rules
Conclusions
References
Author Index

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