This paper presents an open-source pipeline for simulating flow and flow-related processes in (embedded) tubular structures. Addressing a gap in computational fluid dynamics (CFD) and simulation sciences, it facilitates the transition from raw three-dimensional imaging, graph networks or computer aided design (CAD) models of tubular objects to refined, simulation-ready meshes. This transition, traditionally labour-intensive, is streamlined through a series of innovative steps that include surface mesh processing, centre-line construction, anisotropic mesh generation and volumetric meshing, leading to finite element method (FEM) simulations. The pipeline leverages a range of open-source software and libraries, notably GIBBON , FEniCS and Paraview , to provide flexibility and broad applicability across different simulation scenarios, ranging from biomedical to industrial applications. We demonstrate the versatility of our approach through five applications, including the mesh generation for soil–root systems, lung airways, microcirculation networks and portal vein networks, each originating from a different data source. Moreover, for several of these cases, we incorporate CFD simulations and strategies for 3D–1D coupling between the embedding domain and the embedded structures. Finally, we outline some future perspectives aimed at enhancing accuracy, reducing computational time and incorporating advanced modelling and boundary condition strategies to further refine the framework’s capabilities.

The objective of this study is to evaluate the mechanical properties and energy absorption characteristics of the gyroid, dual-lattice and spinodoid structures, as biomimetic lattices, through finite element analysis and experimental characterisation. As part of the study, gyroid and dual-lattice structures at 10 percent volume fraction were 3D-printed using an elastic resin, and mechanically tested under uniaxial compression. Computational models were calibrated to the observed experimental data and the response of higher volume fraction structures were simulated in an explicit finite element solver. Stress-strain data of groups of lattices at different volume fractions were studied and energy absorption parameters including total energy absorbed per unit volume, energy absorption efficiency and onset of densification strain were calculated. Also, the structures were characterized into bending-dominant and stretch-dominant structures, according to their nodal connectivity and Gibson-and-Ashby's law. The results of the study showed that the dual-lattice is capable of absorbing more energy at each volume fraction cohort. However, gyroid structures showed higher energy absorption efficiency and the onset of densification at higher strains. The spinodoid structure was found to be the poorest structure in terms of energy absorption, specifically at low volume fractions. Also, the results showed that the dual-lattice was a stretch dominated structure, while the gyroid structure was a bending dominated structure, which may be a reason that it is a better candidate for energy absorption applications.