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.