Stochastic simulation of pattern formation in growing tissue: a multilevel approach

DOI10.1007/S11538-018-0454-YzbMATH Open1422.92037arXiv1802.01039OpenAlexW2785678880WikidataQ89172395 ScholiaQ89172395MaRDI QIDQ2325569FDOQ2325569

Authors: Stefan Engblom 

Publication date: 26 September 2019

Published in: Bulletin of Mathematical Biology (Search for Journal in Brave)

Abstract: We take up the challenge of designing realistic computational models of large interacting cell populations. The goal is essentially to bring Gillespie's celebrated stochastic methodology to the level of an interacting population of cells. Specifically, we are interested in how the gold standard of single cell computational modeling, here taken to be spatial stochastic reaction-diffusion models, may be efficiently coupled with a similar approach at the cell population level. Concretely, we target a recently proposed set of pathways for pattern formation involving Notch-Delta signaling mechanisms. These involve cell-to-cell communication as mediated both via direct membrane contact sites as well as via cellular protrusions. We explain how to simulate the process in growing tissue using a multilevel approach and we discuss implications for future development of the associated computational methods.

Full work available at URL: https://arxiv.org/abs/1802.01039

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zbMATH Keywords

cell population modelreaction-diffusion master equationsingle-cell modeldiscrete Laplacian cell mechanicsnotch signaling pathway

Mathematics Subject Classification ID

Applications of continuous-time Markov processes on discrete state spaces (60J28) Numerical analysis or methods applied to Markov chains (65C40) Computational methods for problems pertaining to biology (92-08) Cell biology (92C37)

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Cited In (15)

• The Role of Random Structures in Tissue Formation: From a Viewpoint of Morphogenesis in Stochastic Systems
• Stochastic simulation of biochemical systems: in memory of Dan T. Gillespie's contributions
• Exploring the effect of cell heterogeneity in wound healing using a 3D multicellular tissue growth model
• Title not available (Why is that?)
• Roughness and scaling in cellular patterns: Analysis of a simple model
• A framework for modelling and simulating networks of cells
• The emergence of complexity from a simple model for tissue growth
• Particle simulations of morphogenesis
• Analysis of stochastic sensitivity of Turing patterns in distributed reaction-diffusion systems
• Numerical simulation of anisotropic tissue growth using a total Lagrangian formulation
• Invasiveness of a growth-migration system in a two-dimensional percolation cluster: a stochastic mathematical approach
• Computational framework to capture the spatiotemporal density of cells with a cumulative environmental coupling
• On the role of physics in the growth and pattern formation of multi-cellular systems: what can we learn from individual-cell based models?
• On simulating the generation of mosaicism during mammalian cerebral cortical development
• Coupling dynamics of 2D notch-delta signalling

Uses Software

• URDME

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