Title:	Molecular Dynamics Simulation of Protein Translocation in Solid-State Silicon Nitride Nanopores
DNr:	NAISS 2025/22-1108
Project Type:	NAISS Small Compute
Principal Investigator:	Libo Chen <libo.chen@angstrom.uu.se>
Affiliation:	Uppsala universitet
Duration:	2025-08-22 – 2026-09-01
Classification:	10616
Keywords:

Abstract

We propose to perform large-scale molecular dynamics (MD) simulations of protein translocation through solid-state silicon nitride (Si₃N₄) nanopores, focusing on the biomarker C-reactive protein (CRP), an established indicator of systemic inflammation. The objective is to characterize the ionic current blockade signatures generated by CRP during nanopore passage and establish a quantitative link between simulated and experimental current traces. This work will directly support the design and optimization of future solid-state nanopore sensors and will be compared against experimental readouts obtained from similar silicon nitride nanopore systems. The simulations will model a ∼12 nm thick silicon nitride membrane containing a single nanopore of varying diameters (15-20 nm), embedded in explicit electrolyte solution and subject to an applied transmembrane potential. Key observables will include ionic current time series, ion density distributions, protein–pore interaction profiles, and water/ion transport properties. From these, we will extract blockade depth, dwell time, and noise characteristics for direct comparison with experimental datasets.