High Performance Simulations of the Cellular Potts Model

2006 ◽  
Author(s):  
F. Piccini Cercato ◽  
J.C.M. Mombach ◽  
G.G.H. Cavalheiro
Keyword(s):  
Potts Model ◽  
High Performance ◽  
Cellular Potts Model

scholarly journals A minimum energy optimization approach for simulations of the droplet wetting modes using the cellular Potts model

RSC Advances ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 1875-1882
Author(s):  
Ronghe Xu ◽  
Xiaoli Zhao ◽  
Liqin Wang ◽  
Chuanwei Zhang ◽  
Yuze Mao ◽  
...  
Keyword(s):  
Potts Model ◽  
Minimum Energy ◽  
Energy Optimization ◽  
Optimization Approach ◽  
Cellular Potts Model

An optimization approach based on the synthesis minimum energy was proposed for determining droplet wetting modes.

scholarly journals Actin-inspired feedback couples speed and persistence in a Cellular Potts Model of cell migration

2018 ◽  
Author(s):  
Inge M. N. Wortel ◽  
Ioana Niculescu ◽  
P. Martijn Kolijn ◽  
Nir Gov ◽  
Rob J. de Boer ◽  
...  
Keyword(s):  
Cell Migration ◽  
Cell Motility ◽  
Potts Model ◽  
Cell Shape ◽  
Computational Models ◽  
Fundamental Property ◽  
Cellular Potts Model ◽  
Universal Coupling ◽  
Migrating Cells

ABSTRACTCell migration is astoundingly diverse. Molecular signatures, cell-cell and cell-matrix interactions, and environmental structures each play their part in shaping cell motion, yielding numerous different cell morphologies and migration modes. Nevertheless, in recent years, a simple unifying law was found to describe cell migration across many different cell types and contexts: faster cells turn less frequently. Given this universal coupling between speed and persistence (UCSP), from a modelling perspective it is important to know whether computational models of cell migration capture this speed-persistence link. Here, we present an in-depth characterisation of an existing Cellular Potts Model (CPM). We first show that this model robustly reproduces the UCSP without having been designed for this task. Instead, we show that this fundamental law of migration emerges spontaneously through a crosstalk of intracellular mechanisms, cell shape, and environmental constraints, resembling the dynamic nature of cell migration in vivo. Our model also reveals how cell shape dynamics can further constrain cell motility by limiting both the speed and persistence a cell can reach, and how a rigid environment such as the skin can restrict cell motility even further. Our results further validate the CPM as a model of cell migration, and shed new light on the speed-persistence coupling that has emerged as a fundamental property of migrating cells.SIGNIFICANCEThe universal coupling between speed and persistence (UCSP) is the first general quantitative law describing motility patterns across the versatile spectrum of migrating cells. Here, we show – for the first time – that this migration law emerges spontaneously in an existing, highly popular computational model of cell migration. Studying the UCSP in entirely different model frameworks, not explicitly built with this law in mind, can help uncover how intracellular dynamics, cell shape, and environment interact to produce the diverse motility patterns observed in migrating cells.

Topological rearrangements and flow simulation of dry ordered foams

2014 ◽  
Vol 05 (supp01) ◽  
pp. 1441007 ◽  
Author(s):  
J. S. Espinoza Ortiz ◽  
H. Belich ◽  
M. T. D. Orlando ◽  
R. E. Lagos
Keyword(s):  
Strain Rate ◽  
Critical Behavior ◽  
Potts Model ◽  
Driving Force ◽  
Flow Simulation ◽  
Two Dimensional ◽  
Fluid Regime ◽  
Cellular Potts Model ◽  
Flow Through ◽  
Liquid Foam

Flow through a narrow bent channel may induce topological rearrangements in a two-dimensional monodispersed dry liquid foam. We use the Cellular Potts Model to simulate a foam under a variable driving force in order to investigate the strain-rate response from these rearrangements. We observe a set of foams' behaviors ranging from elastic, viscoelastic to fluid regime. Bubble's topological rearrangements are localized and their cumulative rearrangements change linearly with time, thus nonavalanches critical behavior is found. The strain-rate affects the rate of topological rearrangements, its dependence on the drag force is nonlinear, obeying a Herschel–Bulkley-like relationship below the foam's flow point.

Modelling wound closure in an epithelial cell sheet using the cellular Potts model

2015 ◽  
Vol 7 (10) ◽  
pp. 1253-1264 ◽  
Author(s):  
Adrian R. Noppe ◽  
Anthony P. Roberts ◽  
Alpha S. Yap ◽  
Guillermo A. Gomez ◽  
Zoltan Neufeld
Keyword(s):  
Epithelial Cell ◽  
Potts Model ◽  
Wound Closure ◽  
Cell Layer ◽  
Cell Sheet ◽  
Two Dimensional ◽  
Cellular Potts Model ◽  
Epithelial Cell Layer

We use a two-dimensional cellular Potts model to represent the behavior of an epithelial cell layer and describe its dynamics in response to a microscopic wound.

Vascular network formation in silico using the extended cellular potts model

2016 ◽  
Author(s):  
David Svoboda ◽  
Vladimir Ulman ◽  
Peter Kovac ◽  
Barbara Salingova ◽  
Lenka Tesarova ◽  
...  
Keyword(s):  
Potts Model ◽  
In Silico ◽  
Network Formation ◽  
Vascular Network ◽  
Cellular Potts Model

scholarly journals Glassiness in cellular Potts model of biological tissue is controlled by disordered energy landscape

2020 ◽  
Author(s):  
Souvik Sadhukhan ◽  
Saroj Kumar Nandi
Keyword(s):  
Potts Model ◽  
Analytical Study ◽  
Energy Landscape ◽  
Geometric Constraints ◽  
Cellular Potts Model ◽  
Theoretical Understanding ◽  
First Order Transition ◽  
Disordered Energy ◽  
Perimeter Constraint

Glassy dynamics in a confluent monolayer is indispensable in morphogenesis, wound healing, bronchial asthma, and many others; a detailed theoretical understanding for such a system is, therefore, important. We combine numerical simulations of a cellular Potts model and an analytical study based on random first order transition (RFOT) theory of glass, develop a comprehensive theoretical framework for a confluent glassy system, and show that glassiness is controlled by the underlying disordered energy landscape. Our study elucidates the crucial role of geometric constraints in bringing about two distinct regimes in the dynamics, as the target perimeter P0 is varied. The extended RFOT theory provides a number of testable predictions that we verify in our simulations. The unusual sub-Arrhenius relaxation results from the distinctive interaction potential arising from the perimeter constraint in a regime controlled by geometric restriction. Fragility of the system decreases with increasing P0 in the low-P0 regime, whereas the dynamics is independent of P0 in the other regime. The mechanism, controlling glassiness in a confluent system, is different in our study in comparison with vertex model simulations, and can be tested in experiments.

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