(a) Illustration of the integrated framework that synergistically combines scalable modelling using coarse-graining, genetic silk protein synthesis and shear flow spinning process. Mesoscopic DPD simulation snapshots of the recombinant short silk peptides: (b) HAB3, (c) H(AB)2 and (d) HA3B, with coarse-grained representations (top panel), snapshots after equilibration (middle panel) and after shear flow (bottom panel). Hydrophobic ‘a’ beads form aggregates (clusters composed of cross-linked β-crystals via hydrogen bonds) and hydrophilic ‘b’ beads form corona structures around the cluster and physical links between two clusters. The HAB3 solution exhibits small micellar aggregates (<5 nm in diameter), with a minor increase in micelle size after shear. In contrast, the HA3B solution exhibits large micellar aggregates (>10 nm in diameter) with enlarged inhomogeneous globular aggregates after shear (15∼20 nm in diameter), which leads to the clogging of the spinning channel. The H(AB)2 solution exhibits middle-sized homogeneous aggregates (∼ 5 nm in diameter) with enlarged aggregates after shear (∼10 nm in diameter). Note that water beads are not shown for clarity and the scale bar applies for all snapshots. Colour code: red beads—hydrophobic ‘a’ beads in the ‘A’ domain, blue lines—hydrophilic ‘b’ beads in the ‘B’ domain and green lines—hydrophilic ‘b’ beads in the ‘H’ domain.