A Hybrid Parallel Framework for the Cellular Potts Model Simulations

The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6})

On Multiscale Approaches to 3-Dimensional Modeling of Morphogenesis

In this paper we present the foundation of a unified, object-oriented, three-dimensional (3D) biomodeling environment, which allows us to integrate multiple submodels at scales from subcellular to tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model (CPM), with a continuum reaction-diffusion (RD) model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb

Multi-Model Simulations of Chicken Limb Morphogenesis

Early development of multicellular organisms (morphogenesis) is a complex phenomenon. We present COMPUCELL, a multi-model software framework for simulations of morphogenesis. As an example, we simulate the formation of the skeletal pattern in the avian limb bud, which requires simulations based on interactions of the genetic regulatory network with generic cellular mechanisms (cell adhesion, haptotaxis, and chemotaxis). A combination of a rule-based state automaton and sets of differential equations, both subcellular ordinary differential equations (ODEs) and domain-level reaction-diffusion partial differential equations (PDEs) models genetic regulation. This regulation controls the differentiation of cells, and also cell-cell and cell-extracellular matrix interactions that give rise to cell pattern formation and cell rearrangements such as mesenchymal condensation. The cellular Potts model (CPM) models cell dynamics (cell movement and rearrangement). These models couple; COMPUCELL provides an integrated framework for such computations. Binaries for Microsoft Windows and Solaris are available . Source code is available on request, via email: [email protected]