A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis

Computer Physics Communications

Volumn 176, Issue 11-12, 2007, Pages 670-681

  Chen, Nan ^a   Glazier, James A ^b   Izaguirre, Jesús A ^c   Alber, Mark S ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b INDIANA UNIVERSITY   (United States)

^c University of Notre Dame   (United States)

Author keywords

Cellular Potts Model; Computational biology; Morphogenesis; Multiscale models; Parallel algorithms; Pattern formation

Indexed keywords

CELL ADHESION; COMPUTER SIMULATION; NATURAL SCIENCES COMPUTING; PARALLEL ALGORITHMS;

CELLULAR POTTS MODEL; COMPUTATIONAL BIOLOGY; MORPHOGENESIS; MULTISCALE MODELS; PATTERN FORMATION;

CELLS;

EID: 34248201490     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2007.03.007     Document Type: Article

References (21)

1. Graner F., and Glazier J.A. Simulation of biological cell sorting using a two dimensional extended Potts model. Phys. Rev. Lett. 69 (1992) 2013-2016
2. Glazier J.A., and Graner F. Simulation of the differential adhesion driven rearrangement of biological cells. Phys. Rev. E 47 (1993) 2128-2154
3. Weaire D., and Glazier J.A. Relation between volume, number of faces and three-dimensional growth laws in coarsening cellular patterns. Phil. Mag. Lett. 68 (1993) 363-365
4. Chaturvedi R., Huang C., Izaguirre J.A., Newman S.A., Glazier J.A., and Alber M.S. On multiscale approaches to three-dimensional modeling of morphogenesis. J. R. Soc. Interface 2 (2005) 237-253
5. Cickovski T., Huang C., Chaturvedi R., Glimm T., Hentschel H.G.E., Alber M.S., Glazier J.A., Newman S.A., and Izaguirre J.A. A framework for three dimensional simulation of Morphogenesis. IEEE/ACM Trans. Comp. Biol. Bioinform. 3 (2005) 1545-1566
6. Mombach J., and Glazier J.A. Single cell motion in aggregates of embryonic cells. Phys. Rev. Lett. 76 (1996) 3032-3035
7. A.F.M. Marée, From pattern formation to morphogenesis, PhD thesis, Utrecht University, Netherlands, 2000
8. Jiang Y., and Glazier J.A. Foam drainage: Extended large-Q Potts model simulation. Phil. Mag. Lett. 74 (1996) 119-128
9. Jiang Y., Swart P., Saxena A., and Asipauskas J.A. Glazier, hysteresis and avalanches in two dimensional foam rheology simulations. Phys. Rev. E 59 (1999) 5819-5832
10. Mombach J.C.M., Cercato F.P., and Cavalheiro G.H. An efficient parallel algorithm to evolve simulations of the cellular Potts model. Parallel Process. Lett. 15 (2005) 199-208
11. Barkema G.T., and MacFarland T. Parallel simulation of the Ising model. Phys. Rev. E 50 (1994) 1623-1628
12. Gropp W., Lusk E., and Skjellum A. Using MPI: Portable Parallel Programming with the Message Passing Interface. second ed. (1999), MIT Press, Cambridge, MA
13. Gropp W., Lusk E., and Thakur R. Using MPI-2: Advanced Features of the Message-Passing Interface (1999), MIT Press, Cambridge, MA
14. Wright S.A., Plimpton S.J., Swiler T.P., Fye R.M., Young M.F., and Holm E.A. Potts-model grain growth simulations: Parallel algorithms and applications (1997), SAND Report, August 1925
15. Manousiouthakis V.I., and Deem M.W. Strict detailed balance is unnecessary in Monte Carlo simulation. J. Chem. Phys. 110 (1999) 2753-2756
16. Turing A.M. The Chemical Basis of Morphogenesis. Philos. Trans. R. Soc. B (London) 237 (1952) 37-72
17. Stavans J., and Glazier J.A. Soap froth revisited: Dynamical scaling in the two dimensional froth. Phys. Rev. Lett. 62 (1989) 1318
18. Glazier J.A., Anderson M.P., and Grest G.S. Coarsening in the two-dimensional soap froth and the large-Q Potts model: A detailed comparison. Phil. Mag. B 62 (1990) 615
19. Davis G.S., Phillips H.M., and Steinberg M.S. Germ-layer surface tensions and tissue affinities in Rana pipiens gastrulae: Quantitative measurements. Dev. Biol. 192 (1997) 630-644
20. Beysens D.A., Forgacs G., and Glazier J.A. Cell sorting is analogous to phase ordering in fluids. Proc. Natl. Acad. Sci. (USA) 97 (2000) 9467-9471
21. Hentschel H.G.E., Glimm T., Glazier J.A., and Newman S.A. Dynamical mechanisms for skeletal pattern formation in the vertebrate limb. Proc. R. Soc. Lond: Biol. Sci. 271 (2004) 1713-1722