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

Authored by Glen E P Ropella, C Anthony Hunt, Ryan C Kennedy

Date Published: 2016

DOI: 10.1186/s12976-016-0030-9

Sponsors: No sponsors listed

Platforms: MASON

Model Documentation: Other Narrative

Model Code URLs: Model code not found

Abstract

Background: 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. Results: 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. Conclusions: The framework presented in this manuscript expands on existing cell-and agent-centered methods by offering a new perspective in an off-lattice environment. As the demand for biomimetic models grows, the demand for new methods, such as the presented Delaunay and Voronoi framework, is expected to increase.

Tags

Simulation invasion morphogenesis Tumor-growth Multicellular systems Potts-model Differential adhesion Biological cells Single cells Rearrangement