Efficient implementation of a 3-dimensional lattice-free tumor model

The biophysical complexity of tumors can be attacked with numerical models and with the power of modern computers. A numerical model of avascular solid tumors has recently been developed in Trieste and Verona (Milotti E. and Chignola R., PLoS One, 5 (2010) e13942), it includes the basic biology of tumors and it has been successfully validated with experimental data. The model could be further extended and exploited as a tool for understanding tumors and this will require the introduction of new biological details with a consequent increase of the computational effort. Therefore the upgrade of the model requires a prior redesign step. In this paper alternative programming solutions are proposed both for diffusion-reaction part of the code and for the geometrical-topological description of the cell aggregate. These changes will make the code more modular and efficient, and they will make it portable on highly parallel machines.