BioShape: a Uniform Multiscale Approach to Biological System Simulation

Many biological phenomena are inherently multiscale, i.e. they are characterised by interactions in-volving different scales at the same time. Such interactions, even simpler ones, can give rise to emergent properties that only make sense in the context of the system as a whole; at the same time, systems of few interacting components can give rise to complex behaviours that can be missed if all entities, at the different spatial and temporal scales, are not considered. During the last years a large set of approaches have been developed to provide models and sim-ulation frameworks that can help to better understand the basic and advanced dynamics that regulate biological systems. Confronted with a multiscale system, most of the solutions consisted of a series of different models, each of them best suited for a specific resolution level, that were coupled in some way to guarantee a more faithful simulation. In this work we present BioShape, a spatial, geometric, three-dimensional, collision/perception driven simulator that results to be “scale-independent”. It treats any biological entity as a individual entity having a particular 3D shape, equipped with perception capabilities, moving in the simulation space through a personalised motion law, and colliding with other entities giving rise to bounces or to joined entities. Such a model is naturally uniform as different resolution levels can all be modelled in terms of shapes and interactions among them. The model is also information lose-less since passage from a scale level to another is reduced to a mapping between different granularity instances of the same (shape based) model. To better underline the features provided by BioShape it has been applied in two case studies: an aortic valve and the bone remodelling process that occurs in any skeleton-enabled living being.