13th International Conference on Membrane Computing - MTA Sztaki

<strong>13th</strong> <strong>International</strong> <strong>Conference</strong> on Membrane Computing, CMC13,
Budapest, Hungary, August 28 - 31, 2012. Proceedings, pages 407 - 418.
Observer/Interpreter P Systems
Dragos Sburlan
Ovidius University of Constanta
Faculty of Mathematics and Informatics
Constanta, Mamaia 124, Romania
Abstract. In this paper we discuss Observer/Interpreter P systems,
i.e., a model of computation inspired by the possibility of tracking and
detecting fluorescent proteins in living cells and interpreting the results
by visualizing molecular events in real time. In this regard, we define
Observer/Interpreter P systems as a couple of two independent systems:
a P system with symbol objects and multiset rewriting rules and a finite
state machine able to perform an operation (addition/subtraction) on
a register. We investigate the computational power of the model when
different features are taking into account.
Keywords: P Systems, Observation, Interpretation
1 Introduction
One important breakthrough in the study of living cells was the possibility to
label proteins for imaging use. This was achieved by using some genetically encoded
fluorescent fusion tags (for instance, the Nobel Prize in Chemistry in 2008
was awarded to Osamu Shimomura, Martin Chalfie and Roger Tsien for the
discovery and development of green fluorescent protein – GFP, that was used
by researchers to study the development of nerve cells in the brain or how cancer
cells spread). The gene for GFP was originally isolated from the jellyfish,
Aequorea victoria, and since then, a lot of scientific effort has been focused on
the discovery of processes occurring inside cells. By visualizing molecular events
happening within the living cells one can trace the molecules function and regulation.
In general, the common methods for labeling molecules in biological
systems are based on the genetic fusion of fluorescent tags. Using these tags one
can watch at nanometer scale the behavior of molecules (the movement, positions,
and interactions), hence one can unravel the regulatory mechanisms of
biological systems.
Nowadays, the code for GFP can be inserted at any given position in the
genome and once there, it will act as a label for the other genes around it.
Accordingly, one can place a GFP gene next to a given gene of interest and then
study how the corresponding protein behaves by watching the green fluorescence.
Moreover, the sequence of aminoacids in the GFP can be genetically engineered
such that it will produce fluorescent proteins glowed in many different colors.
In this way, several distinct types of proteins can be marked by different colors,
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