A cell-centered, agent-based framework that enables flexible environment granularities

Theoretical Biology & Medical Modelling
Ryan C KennedyC Anthony Hunt

Abstract

Mechanistic explanations of cell-level phenomena typically adopt an observer perspective. Explanations developed from a cell's perspective may offer new insights. Agent-based models lend themselves to model from an individual perspective, and existing agent-based models generally utilize a regular lattice-based environment. A framework which utilizes a cell's perspective in an off-lattice environment could improve the overall understanding of biological phenomena. We present an agent-based, discrete event framework, with a demonstrative focus on biomimetic agents. The framework was first developed in 2-dimensions and then extended, with a subset of behaviors, to 3-dimensions. The framework is expected to facilitate studies of more complex biological phenomena through exploitation of a dynamic Delaunay and Voronoi off-lattice environment. We used the framework to model biological cells and to specifically demonstrate basic biological cell behaviors in two- and three-dimensional space. Potential use cases are highlighted, suggesting the utility of the framework in various scenarios. The framework presented in this manuscript expands on existing cell- and agent-centered methods by offering a new perspective in an off-lattice envir...Continue Reading

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Citations

Oct 8, 2020·Bulletin of Mathematical Biology·Sonja MathiasAndreas Hellander

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Software Mentioned

ABM
Virtual Cell
VTK
Chaste
MASON
Visualization Toolkit ( VTK )

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