NewtonBioMorphX: A computational framework for simulating tissue-scale mechanics of morphogenesis
Description
The self-organised morphogenesis of multicellular organisms emerges not only from biochemical but also from mechanical processes operating across spatial scales. Yet, computational tools for simulating tissue-scale mechanics have largely been released as restricted, study-specific codes. Here, we present NewtonBioMorphX, a GPU-accelerated, open-access comprehensive framework for simulating tissue-scale mechanical morphogenesis. Built on a finite-strain finite-element formulation on tetrahedral meshes, the software implements an unusually broad set of mechanical ingredients: isotropic and anisotropic (direction-specific) growth; multi-layer tissue mechanics; neo-Hookean hyperelasticity combined with stretch-based plasticity; Kelvin–Voigt viscoelasticity; passive anisotropic fibres emulating 3D collagen networks; anisotropic active contractile filaments emulating actin; Hertzian contact forces; and multiple orthonormal coordinate bases (Cartesian, normal–tangent, cylindrical, spherical, cone-adapted, and toroidal). Equally central is an extensive, user-friendly graphical interface spanning the entire workflow — mesh generation from geometric primitives or arbitrary mesh input, per-layer material and growth specification (including analytical functions of space and time compiled at runtime), boundary-condition assignment, real-time colour-mapped and glyph-based visualisation of scalar and tensor fields, and structured data export — allowing intricate mechanical modelling of morphogenetic processes without editing or recompiling source code. The NewtonBioMorphX framework is validated using a benchmark implementing the well-known Cook’s membrane problem, and its versatility is illustrated through parameter gradient plots, as well as twelve ready-to-run preset examples spanning diverse morphologies.