An efficient cellular Potts model algorithm that forbids cell fragmentation

DOI10.1016/J.CPC.2016.07.030MaRDI QIDQ1682765zbMATH OpenOpenAlexFDO

Authors Marc Durand, Etienne Guesnet

Publication date 5 December 2017

Published in Computer Physics Communications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1609.03832

zbMATH Keywords

latticeMonte Carlocellular Potts modelcellular systems

Mathematics Subject Classification ID

Probabilistic models, generic numerical methods in probability and statistics (65C20) Dynamic lattice systems (kinetic Ising, etc.) and systems on graphs in time-dependent statistical mechanics (82C20) Cell biology (92C37) Applications to the sciences (65Z05)

Abstract: The Cellular Potts Model (CPM) is a lattice based modeling technique which is widely used for simulating cellular patterns such as foams or biological tissues. Despite its realism and generality, the standard Monte Carlo algorithm used in the scientific literature to evolve this model preserves connectivity of cells on a limited range of simulation temperature only. We present a new algorithm in which cell fragmentation is forbidden for all simulation temperatures. This allows to significantly enhance realism of the simulated patterns. It also increases the computational efficiency compared with the standard CPM algorithm even at same simulation temperature, thanks to the time spared in not doing unrealistic moves. Moreover, our algorithm restores the detailed balance equation, ensuring that the long-term stage is independent of the chosen acceptance rate and chosen path in the temperature space.

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Cites work

• scientific article; zbMATH DE number 1782878 (Why is no real title available?)
• Improving the realism of the cellular Potts model in simulations of biological cells
• Parallelizing the cellular Potts model on graphics processing units
• Single-cell-based models in biology and medicine.

Cited in

(5)

• A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis
• Multiscale extensions of the cellular Potts models: toward a nested-hybrid approach
• Improving the realism of the cellular Potts model in simulations of biological cells
• Parallelizing the cellular Potts model on graphics processing units
• A 3D computational study on the formation and progression of tumor cells in diffuse gastric cancer

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