Molecular Mechanisms of Spontaneous Peptide Translocation through BC ₃ /C ₃ N Heterostructure Nanopores: A Molecular Dynamics Study

Solid-state nanopore (SSN) sequencing has emerged as a revolutionary technique in genetic and proteomic analysis, offering low costs and long read-lengths. However, traditional SSN sequencing, which relies on an electric field to drive biomolecules, faces challenges in translocating nonuniformly charged proteins, limiting its application in single-molecule protein sequencing. In this work, molecular dynamics (MD) simulations were employed to investigate peptide translocation across a BC₃/C₃N van der Waals (vdW) heterostructure nanopore in the absence of external forces. Our results revealed that the peptide spontaneously translocates from the BC₃ surface to the C₃N surface due to stronger binding on the latter. However, the translocation is temporarily impeded by aromatic Phe residues, which experience strong π-π interactions with nanosurfaces, creating significant energy barriers for Phe desorption. These findings clarify the molecular-scale interactions that govern peptide motion across the BC₃/C₃N heterostructure interface and reveal how asymmetric adsorption energetics enable spontaneous, directional transport. Rather than assessing sequencing feasibility, this study provides mechanistic insights into heterostructure-mediated peptide motion and establishes a conceptual framework for future investigations of nanopore-based biomolecule manipulation.