Journal
COMPUTER PHYSICS COMMUNICATIONS
Volume 176, Issue 11-12, Pages 670-681Publisher
ELSEVIER
DOI: 10.1016/j.cpc.2007.03.007
Keywords
computational biology; morphogenesis; parallel algorithms; cellular Potts model; multiscale models; pattern formation
Funding
- NIGMS NIH HHS [R01 GM076692, R01 GM077138-01A1, R01 GM076692-01, R01 GM076692-03, R01 GM076692-02] Funding Source: Medline
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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.
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