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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.

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is a doctoral student in Bioengineering at the University of Utah. His research interests are incomputational electrophysiology, scientific visualization, bioelectric signal processing and electrocardiographic mapping.Kedar has worked as an engineer at Whirlpool and also has MS in computer science from the University of Notre Dame.

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