title: Simulating colonial growth of fungi with the Neighbour-Sensing model of hyphal growth.
abstract: The Neighbour-Sensing model brings together the basic essentials of hyphal growth kinetics into a vector-based mathematical model in which the growth vector of each virtual hyphal tip is calculated by reference to the surrounding virtual mycelium. The model predicts the growth pattern of many hyphae into three spatial dimensions and has been used to simulate complex fungal fruit body shapes. In this paper we show how the Neighbour-Sensing model can simulate growth in semi-solid substrata like agar or soil, enabling realistic simulation of mycelial colonies of filamentous fungi grown in 'Petri-dish style' experimental conditions. Newly implemented capabilities in the model include: a measurement and logging system within the program that maintains basic statistics about the mycelium it is simulating, this facilitates kinetic experimentation; inclusion of 'substrates' in the data space causing positive or negative tropisms for the growing mycelium; a horizontal plane tropism that provides a way of simulating colonies growing in or on a substratum like agar or soil by imposing a horizontal constraint on the data space the cyberhyphal tips can explore; three categories of hypha--standard hyphae are those that start the simulation, leading hyphae can emerge from the colony peripheral growth zone to take on a leading role, and secondary hyphae are branches that can arise late, far behind the peripheral growth zone, when mature hyphal segments resume branching to in-fill the older parts of the colony. We show how the model can be used to investigate hyphal growth kinetics in silico in experimental scenarios that would be difficult or impracticable in vivo. We also show that the Neighbour-Sensing model can generate sufficiently realistic cord-like structures to encourage the belief that this model is now sufficiently advanced for parameters to be defined that simulate specific in silico cyberfungi. The potential utility of these cyberspecies is that they provide a means to model the morphogenetic effects of a variety of factors, from environmental and nutritional features to mutations, in experimentally realistic situations, offering a valuable addition to the experimental toolkit of all those interested in fungal growth and morphology.
authors.affiliation: School of Biological Sciences, Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
authors.forename: Audrius
authors.initials: A
authors.lastname: Meskauskas
authors.forename: Mark D
authors.initials: MD
authors.lastname: Fricker
authors.forename: David
authors.initials: D
authors.lastname: Moore
mesh_terms: D003196:Computer Graphics; D003198:Computer Simulation; D005658:Fungi / Q000254:growth & development*; D025301:Hyphae / Q000254:growth & development; D008954:Models, Biological; D008962:Models, Theoretical