The self-assembly of vertically aligned block copolymer (BCP) cylinders becomes more difficult when their minority block possesses a lower surface tension than majority block. Because of this specific characteristic, these inverse cylinder systems are highly susceptible to kinetic trapping in thin film geometries. While coarse-grained (CG) molecular dynamics (MD) simulations utilizing hard-wall substrates — where substrate beads are frozen in their initial place but modeled to mimic a random copolymer brush that facilitates vertical orientation — successfully capture the formation of vertical inverse cylinders, their rigid boundaries do not readily accommodate localized relaxation, limiting the statistical likelihood of sampling the fully aligned morphology. To facilitate the sampling of vertically oriented inverse cylinders in MD, we introduced an extended CGMD model featuring a mechanically compliant, harmonically tethered soft substrate. Across an ensemble of independent replicas, the soft boundary allowed interfacial chains to relieve vertical compressive strain, evidenced by a significantly reduced radius of gyration. By enabling localized reorganization, this mechanical buffering shifted the morphological yield toward higher structural fidelity compared to the hard-wall baseline. Ultimately, by substantially increasing both the maximum vertical orientation metric and the peak topological cylinder count, this study demonstrates that incorporating substrate compliance is a critical computational strategy for promoting structural rearrangement and reliably sampling defect-free vertical arrays of inverse cylinders in MD simulations.

Keywords: Block Copolymer, Self-Assembly, Inverse Cylinders, Molecular Dynamics Simulation