MODELING AND SIMULATION OF CELL-CELL COMMUNICATION WITH PETRI NETS ?

rumblecleverAI and Robotics

Dec 1, 2013 (3 years and 17 days ago)

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MODELING AND SIMULATION OF CELL
-
CELL

COMMUNICATION
WITH PETRI NETS

?

R. Hofestädt

AG Bioinformatics and Medical Informatics, University Bielefeld, Bielefeld, Germany

Email:
hofestae@techfak.uni
-
bielefeld.de


Keywords:

Modeling and s
imulation, cell communication, cell differentiation, Petri nets.


Motivation

Until now the
focus of Bioinformatics is the function of a cell. To understand the molecular
mechanisms of life we
also
need to

understand the cell
-
cell communication and cell differentiation
processes. Checking the
available

literature
,

we can see that
many
different
formal systems are
published to

model metabolic process
es. During the last decade

has been shown

that the Petri net
formalism
is useful

for this kind of modeling and simulation. The main advantages
of Petri nets are:
1)

powerful

theory
2)

and

simulati
on environments

are
available
. Furthermore
,

it is possible

to start
the
modeling process
with a simple

discret
e

Petri net model
,

which can be extended anytime using
kinetic p
arameters (functional Petri nets

etc.).
Contemplating

modeling of cell
-
cell communication
and cell differ
entiati
on processes we can see specific

appli
cations of the cellular automaton

and
/or

the L
-
Sy
stems. The
cellular automaton

was exactly defined
to model
simple communi
cation
processes. The L
-
Systems

were

defined by Lindenmayer only to model and simulate cell
differentiation processes. Therefore
,

Lindenmayer defined parallel grammars
which can exactly
realize th
is kind of simulation processes.


Aim and method

This presentation

will discuss the question
if

the Petri net
can

also be used for the modeling of cell
-
cell communication processes.

Therefore we will discuss how we can extend Petri nets so that the
communic
ation
between

different Petri nets will be possible. W
e will develop
and discuss
different
topologies of Petri

net structures
. Furthermore we will discuss the question if these kin
ds of Petri
nets are useful to solve practical questions.

Application

In our case we will use the Quorum Sensing process of t
he bacteria to demonstrate

how this kind of
simulation can be used and can be useful for the solution of scientific questions.


Li
terature

M.
Chen,

S. Hariharaputran, R. Hofestädt, B. Kormeier, S.

S
pangardt.
(2009)

Petri net models for the semi
-
automatic construction of
large scale biological networks,

Springer Science and Business. Journal 11047, Article
9151.