Using Design Patterns in Scientific Applications

Revision with unchanged content. Design Patterns have been widely adopted for building flexible and extensible applications.

However, this can come at a cost of reduced performance, which may not be acceptable for computationally intensive scientific applica-tions.

Therefore, the effects of design patterns on application performance are investigated through a detailed measurement and profiling of CompuCell3D. It is a software framework for three-dimensional modeling (3D) of morpho-genesis, which is a stage in embryonic development where cells cluster into tissues and organs.

By reverse engineering CompuCell3D subsystems with and without design patterns, their impact on application performance and-maintainability is evaluated. Finally, CompuCell3D functionality is extended to support irregular domains for biologically realistic simulations.