A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis
A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis
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DOI：
10.1016/j.cpc.2007.03.007
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发表时间：
2007-06-01
影响因子：
6.3
通讯作者：
Alber, Mark S.
中科院分区：
文献类型：
--
作者：
Chen, Nan;Glazier, James A.;Alber, Mark S.
细胞Potts模型（CPM）已被用于各种各样的生物模拟。然而，目前大多数CPM实现使用顺序修改的大都会算法，限制了模拟的大小。在本文中，我们提出了一个并行CPM算法模拟形态发生，其中包括细胞-细胞粘附，细胞体积的限制，和细胞haptotaxis。该算法使用适当的数据结构和棋盘形子网格的并行化。通信和更新算法同步不同的处理器节点上模拟的细胞的属性。实验表明，该并行算法具有良好的可扩展性，可用于大规模细胞形态发生（10（7）个或更多个细胞）的模拟，拓宽了CPM的应用范围。新算法满足平衡条件，这是充分的底层马尔可夫链收敛。(c)2007 Elsevier B. V.保留所有权利。
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. (c) 2007 Elsevier B.V. All rights reserved.