Simulation Based Analysis of Nanocarrier Internalization: Exciting Challenges with a New Computational Tool - Intracellular Delivery: Fundamentals and Applications - page 136

GENERIC SIMULATOR

EXPERT PROGRAM
transition functionalities
(transformations,
transports, rules)
states functionalities
(accounting,
overwriting)

Expert

K
E
R
N
E
L

USER PROGRAM
transition elements
state elements
reading channels
modifying channels

User

Fig. 4 Computer implementation of direct computer mapping

The recent implementation of the above architecture is written in GNU-Prolog
( http://www.gprolog.org/ ), because the free unification of the high-level structures,
contained in dynamic partitions, supports the methodology. Temporarily, we use a
GraphViz ( http://www.graphviz.org/ ) based configurable input/output user inter-
face (Varga 2009 ). This is a platform-independent and partly open software tool,
consisting of a general kernel, communicating with expert and user interfaces.
The software implementation can be applied for the simulation of multi-scale
hybrid (discrete/continuous, quantitative/qualitative, deterministic/stochastic) pro-
cesses. In hybrid models, the communication of the different parts can be supplied
with the necessary transforming operators.

3.2 DCM Description of the Internalization Problem

In the temporarily used software implementation of Direct Computer Mapping,
first we edit the structure of the model by the open source code GraphViz tool that
generates a script. The graphically edited structure of the discussed model
(see Fig. 1 ) is shown in Fig. 5 . In this graphical representation