Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts ModelĬellular Potts models (CPMs) are used as a modeling framework to elucidate mechanisms of biological development. The phase transition of the glassy Potts model is easily interpreted as the spin-glass transition of the ordinary random Potts model. Both models do not exhibit any spontaneous magnetization at low temperature, differently from the ordinary glass Potts model.
and the ``chiral Potts model'' investigated by Nishimori and Stephen. We report the equivalence of the ``glassy Potts model,'' recently introduced by Marinari et al. All rights reserved.Ĭomment on ``Glassy Potts model: A disordered Potts model without a ferromagnetic phase'' We finally predict shapes and forces for micropatterns that have not yet been experimentally studied. We then demonstrate that it is in good agreement with experimental data for shape, spreading dynamics, and traction force patterns of cells on micropatterned substrates. We first parameterize our model and show that it accounts for momentum conservation. To account for local contour reinforcement by peripheral bundles, we augment the cellular Potts model by elements of the tension-elasticity model. The third dimension is treated as an area reservoir for spreading. To predict the dynamics and steady states of cell shape and forces without any a priori knowledge of how the cell will spread on a given micropattern, here we extend earlier formulations of the two-dimensional cellular Potts model. Moreover, they are increasingly used in combination with traction force microscopy on soft elastic substrates. Micropatterned substrates are often used to standardize cell experiments and to quantitatively study the relation between cell shape and function. 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.ĭynamics of cell shape and forces on micropatterned substrates predicted by a cellular Potts model. 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. This allows to significantly enhance realism of the simulated patterns. We present a new algorithm in which cell fragmentation is forbidden for all simulation temperatures. 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. 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. The hybrid parallel CPM can be used for the large scale simulation ().« lessĪn efficient Cellular Potts Model algorithm that forbids cell fragmentation The application and performance analysis show that the hybrid parallel framework is quite efficient.
Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model.
LIFTOFF SIMULATOR LIBREPILOT SYNC UPDATE
Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approachmore » achieves good performance and high accuracy at the same time. The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI).
In this paper we present a hybrid parallel framework for CPM simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. The Cellular Potts Model (CPM) has been widely used for biological simulations.
A hybrid parallel framework for the cellular Potts model simulations
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