Solid-State Nanopores with Atomically Smooth Surface for ssDNA Transport Alex Smolyanitsky ∗ Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO 80305, USA Binquan Luan † IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY, 10598, USA (Dated: November 13, 2021) Engineered protein nanopores have been demonstrated to be promising candidates for de-novo high-throughput, low-cost DNA sequencing. Their solid-state analogs, on the other hand, remain lacking for this application due to poorly controllable surface structures and nonspecific nucleotide- nanopore interactions. Resolving these challenges is key to achieving reliable detection of nucleotide- specific electrical signals in nanoscale DNA readers. Here, using density functional theory calcu- lations, we demonstrate that nanopores in bilayer hexagonal boron nitride possess an atomically smooth surface, seamlessly connecting the two stacked hexagonal lattices. Using all-atom molecu- lar dynamics simulations, we demonstrate low-friction electrophoretic transport of aqueous ssDNA through such bilayer-hBN nanopores. We unveil the fundamental mechanisms underlying the ob- served continuous ssDNA transport across these pores and explain why they present a more favorable environment for ssDNA transport in comparison with monolayer hBN-based nanopores featuring abrupt or disordered edges. Nanopore-based sensing of DNA nucleotides is becom- ing essential to human genome sequencing [1] and the recently proposed DNA storage technologies [2]. Af- ter decades of extensive studies, protein-nanopore-based DNA sequencing is poised to become a low-cost, high- throughput complement or possibly replacement for the existing technologies, including the now-ubiquitous dye sequencing [3] and the Sanger method [4]. In the mean- time, the use of solid-state nanopores (nanoscale orifices in thin SiO 2 or Si 3 N 4 membranes) for sequencing remains challenging. Despite significant merits, such as chemi- cal and mechanical robustness, solid-state nanopores suf- fer several serious drawbacks that limit their applica- tion. For example, a typical solid-state nanopore drilled with a focused electron or ion beam usually has poorly controllable geometric and surface properties (such as hydrophobicity and charge density). Consequently, the pore-to-pore variation in these properties limits the re- liability of measured electrical currents used in sequenc- ing and ultimately reduces detection accuracy [5, 6]. In order to achieve solid-state nanopores with well-defined atomic structures similar to the ones in transmembrane proteins, various two-dimensional (2D) materials have been proposed as host membranes [7–10]. In particu- lar, electrophoretic transport of DNA through graphene- and hexagonal boron nitride (hBN)-based nanopores has been studied extensively. So far, most cases of successful transport were demonstrated with double-stranded DNA (dsDNA) [7, 9, 10]. Transport of single-stranded DNA (ssDNA), especially useful for sequencing, however, has proven to be more difficult in experiments [11]. Recent advances in fabrication have yielded atomically sculpted nanopores in molybdenum disulfide (MoS 2 ) monolayers, enabling a well-controlled pore geometry [12]. Never- theless, continuous transport of a long ssDNA molecule through nanopores in 2D nanosheets remains challenging due to fundamental limitations arising from non-specific adsorption of DNA bases in and around nanopores, caus- ing pore clogging. In addition, pores in 2D-membranes are atomically thin, presenting an atomically sharp dis- continuity for ssDNA adsorbed on a 2D nanosheet to tra- verse during its movement from one surface of the sheet to the other. In order to overcome this limitation, here we propose a nanopore with an atomically defined toroidal surface, which facilitates relatively low-friction (resulting from a low energy barrier) transport of ssDNA through an atomically thin membrane. Previously, we studied nanopores in 2D heterostruc- tures formed by stacking a graphene monolayer upon an MoS 2 monolayer [13]. Although nanopores in such het- erostructures have a finite height, the complexity of inter- layer interactions limits the overall promise in achieving predictable pore edge properties. Here, we investigate the edge surface of a hexagonal nanopore in an AA’-stacked hBN bilayer. Using density functional theory (DFT) cal- culations, we show that the optimized structure of such a pore features covalent B-N fusing between layers, re- sulting in an atomically smooth toroidal edge. Using density functional theory molecular dynamics (DFTMD), we demonstrate that the pore structure is stable at room temperature. Finally, using all-atom molecular dynam- ics (MD) informed by our DFT calculations, we demon- strate that an ssDNA molecule can be electrophoretically driven across this nanopore at a low biasing voltage. For comparison, this process is shown to be impossible in an identical system, except featuring a similarly sized pore in monolayer hBN. From analyzing the transport dy- namics and energetics, we demonstrate nonequilibrium low-friction sliding of ssDNA through hBN bilayer-based nanopores, in contrast with asperity-like (high-friction) arXiv:2011.00408v1 [cond-mat.mes-hall] 1 Nov 2020