#38 · Systems biology

Mechanical and diffusive forces modelled as generators of tissue and pattern geometry

The dominant thread is an explicit physical mechanism, mechanical or diffusive, that generates biological geometry in simulation. A coupled vertex-flow model attributes lumen formation, budding, and branching to hyaluronic acid osmotic pressure in intercellular space. A 3D cell-fiber model reproduces adipose tissue architectures and their heterogeneity in silico. A two-stage diffusion-driven model reproduces diatom silica rib branching and pore formation on a finite element mesh, with evolving connectivity. A topoietic diffusion-decay stress-signal model, calibrated to Xenopus embryo group data, reproduces cross-embryo rescue rates. A focal adhesion-actomyosin model adds a molecular layer, with ECM stiffness history steering adhesion mode selection. What is new is the explicit linkage of mechanism to emergent geometry, demonstrated here most directly by the diatom model's evolving connectivity. All items are preprints reporting model-based reproduction rather than experimental comparison.