Chen Nan, Glazier James A, Izaguirre Jesús A, Alber Mark S
Department of Mathematics, University of Notre Dame, Notre Dame, IN 46556, USA.
Comput Phys Commun. 2007 Jun;176(11-12):670-681. doi: 10.1016/j.cpc.2007.03.007.
The Cellular Potts Model (CPM) has been used in a wide variety of biological simulations. However, most current CPM implementations use a sequential modified Metropolis algorithm which restricts the size of simulations. In this paper we present a parallel CPM algorithm for simulations of morphogenesis, which includes cell-cell adhesion, a cell volume constraint, and cell haptotaxis. The algorithm uses appropriate data structures and checkerboard subgrids for parallelization. Communication and updating algorithms synchronize properties of cells simulated on different processor nodes. Tests show that the parallel algorithm has good scalability, permitting large-scale simulations of cell morphogenesis (10(7) or more cells) and broadening the scope of CPM applications. The new algorithm satisfies the balance condition, which is sufficient for convergence of the underlying Markov chain.
细胞Potts模型(CPM)已被广泛应用于各种生物模拟中。然而,当前大多数CPM实现都使用顺序修改的Metropolis算法,这限制了模拟的规模。在本文中,我们提出了一种用于形态发生模拟的并行CPM算法,该算法包括细胞间粘附、细胞体积约束和细胞趋触性。该算法使用适当的数据结构和棋盘子网格进行并行化。通信和更新算法同步在不同处理器节点上模拟的细胞属性。测试表明,并行算法具有良好的可扩展性,允许对细胞形态发生进行大规模模拟(10^7个或更多细胞),并拓宽了CPM应用的范围。新算法满足平衡条件,这对于基础马尔可夫链的收敛是足够的。