Artificial Cell Systems Based in Gene Expression Protein Effects - Advancing Artificial Intelligence Through Biological Process Applications - page 152

Box A.

FOR every Protein at the cytoplasm do
TTL j = TTL j - 1;
IF (TTL j = 0)
P i = P i - 1; protein j Є Type i
ENDIF
ENDFOR

WHILE no New Cycle DO

FOR each genes promoter
Return %P a = (P a / ∑ P b ) * 100
a, b Є 1,N
ENDFOR

IF Requirement a type protein AND P a > 0
P a = P a - 1;
ENDIF
ENDDO

after the recovery of the necessary proteins from
the cytoplasm and the generation of the encoded
proteins in the selected genes. Once the genes
are transcribed with the generated proteins, it is
determined which cellular reactions accompany
them: every protein can either be communicated
to a neighbour cell, stored in the cytoplasm, or
carry out one of the special actions of a mitosis
or an apoptosis. The behaviour of the cytoplasm
in each cycle of the system can be seen in the
pseudo-code in Box A, where P x identifies the
number of x type-proteins and TTL y represents
the lifetime of the y type-protein.
According to this pseudo-code, the cyto-
plasm starts by updating the lifetime of its
stored proteins and then returns the informa-
tion on the concentrations of the system's N
proteins. Importantly, the concentration is
used to calculate the genes activation. The
cytoplasm concentration of proteins decreases
when they are required for genes transcription,
which may coincide with specific actions.
When all the possible actions of the cellular

cycle are terminated, the process restarts by
updating the cytoplasm with the proteins iden-
tified for storage and those received through
communications with neighbour cells during
the previous cycle.

Genome Evaluation

A classical approach of EC proposes the use
of Genetic Algorithms (GA) (Fogel, Owens &
Walsh, 1966; Goldberg, 1989; Holland, 1975) for
the optimisation, in this case, of the values of the
DNA genes (binary strands). Each individual of
the GA population will represent a possible DNA
strand for problem solving.
In order to calculate the fitness value for every
individual in the GA or the DNA, the strand is
introduced into an initial cell or zygote. After
simulating during a certain number of cycles,
the contained information is expressed and the
characteristics of the resulting tissue are evalu-
ated by means of various criteria, according to
the goal that is to be achieved.