diploma sebastian schneider


The goal of the diploma thesis “Entwicklung einer Schnittstelle zur Integration membranberechnender Algorithmen in den CELLmicrocosmos2.1” was to develop an Interface for the CELLmicrocosmos 2.1 program that allows to embed algorithms for membrane-calculation. With this interface it should be possible to integrate self developed algorithms using methods like Molecular Dynamics, Monte-Carlo or whichever serve the demands.


In former versions of the CELLmicrocosmos 2 program (Cm2 / Cm2.1) there were predefined ways to calculate the membrane. They had been accurate for generating large membranes with high speed but ignored scientific methods.

Another insufficiency was that this methods where proper for some aims but dissatisfying for other interests. Coming to the conclusion that there is no possibility to create a method that is on the one hand fast and on the other hand adequate to all interests the idea was formed that a plug-in structure could help out of this predicament.

diploma prolog

Therefore some subgoals had to be finalized. One was the internal and graphical representation of the molecules. The former two dimensional representation was raised to a three dimensional using Java3D. Resultant three dimensional calculations could be realized.
Another point was the unclear structure of the molecules. They contain a lot of information unnecessary for the calculation of membranes. Wrapping classes hide these informations and present only relevant data.


The main part of the diploma was the development of the interface. This is defined by a protocol, a plug-in manager and a package of methods. The protocol defines how algorithm should be structured so that they can be included into the CELLmicrocosmos 2.1 program.

The plug-in manager allows to load and run algorithms in the CELLmicrocosmos2.1 program. A last point are the methods which handle the consistency between internal and graphical representation. Also a lot of basic methods are included helping to create and delete molecules, detect collisions, measure distances, etc.

Another part of the diploma was the creation of membrane-calculating algorithms. Therefore three algorithms had been written which are basically included into the Cm 2.1 program. One very fast but without dynamic, one with more dynamic but still fast and one more complex but costly in terms of time algorithm based on a Simulated-Annealing Algorithm resemble Monte-Carlo probability methods.

Sebastian Schneider

Cm_ss_vortrag25022008 (pdf)
- the presentation took place at the 25th February 2008 (german)

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