title: PAM: Particle automata model in simulation of Fusarium graminearum pathogen expansion.
abstract: The multi-scale nature and inherent complexity of biological systems are a great challenge for computer modeling and classical modeling paradigms. We present a novel particle automata modeling metaphor in the context of developing a 3D model of Fusarium graminearum infection in wheat. The system consisting of the host plant and Fusarium pathogen cells can be represented by an ensemble of discrete particles defined by a set of attributes. The cells-particles can interact with each other mimicking mechanical resistance of the cell walls and cell coalescence. The particles can move, while some of their attributes can be changed according to prescribed rules. The rules can represent cellular scales of a complex system, while the integrated particle automata model (PAM) simulates its overall multi-scale behavior. We show that due to the ability of mimicking mechanical interactions of Fusarium tip cells with the host tissue, the model is able to simulate realistic penetration properties of the colonization process reproducing both vertical and lateral Fusarium invasion scenarios. The comparison of simulation results with micrographs from laboratory experiments shows encouraging qualitative agreement between the two.
authors.affiliation: AGH University of Science and Technology, 30-059 Kraków, Poland. Electronic address: wcislo@agh.edu.pl.
authors.forename: Rafał
authors.initials: R
authors.lastname: Wcisło
authors.affiliation: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON Canada, K1A 0C6. Electronic address: shea.miller@agr.gc.ca.
authors.forename: S Shea
authors.initials: SS
authors.lastname: Miller
authors.affiliation: AGH University of Science and Technology, 30-059 Kraków, Poland. Electronic address: dzwinel@agh.edu.pl.
authors.forename: Witold
authors.initials: W
authors.lastname: Dzwinel
mesh_terms: D000465:Algorithms; D001696:Biomechanical Phenomena; D002473:Cell Wall / Q000502:physiology; D019295:Computational Biology; D003198:Computer Simulation; D005670:Fusarium; D015966:Gene Expression Regulation, Fungal; D021621:Imaging, Three-Dimensional; D008954:Models, Biological; D010935:Plant Diseases / Q000382:microbiology*; D013314:Stress, Mechanical; D014908:Triticum / Q000382:microbiology*
keywords: Cellular Automata; F. graminearum proliferation; Multi-scale simulations; Particle automata model; Particle model