How We Simulate Nanopores

Nanopore technology has revolutionized single-molecule science by enabling ultrasensitive characterization of biomolecular structure and interactions via accessible, physics-based tabletop measurements. In a typical experiment, the chemical structure of a biomolecule is determined by measuring a transient blockade of the nanopore ionic current produced by the nanopore passage of the molecule. Nanopore sensing can now deliver a telomere-to-telomere sequence of a human chromosome and is poised to unravel the vast complexity of the proteome. Notwithstanding the three decades of development, a fundamental interpretive bottleneck remains: the method cannot independently determine the 3D structure of a biomolecule as it passes through the nanopore. All-atom molecular dynamics has emerged as a go-to method for determining the structure of the translocating molecules and its relationship with the nanopore current. Here, we review molecular dynamics methods used to simulate the transport through biological, solid-state, and DNA origami nanopores. We highlight how advances in high-performance computing and enhanced sampling are dismantling historical timescale barriers, allowing the simulations to achieve unprecedented experimental relevance. By detailing the path from system construction to the extraction of experimental observables, we illustrate how computational insights are transitioning from providing post-hoc signal interpretation to enabling predictive, rational design of next-generation biosensors.