SUPR
Molecular Dynamics Simulation of Protein Translocation in Solid-State Silicon Nitride Nanopores
Dnr:

NAISS 2025/22-1108

Type:

NAISS Small Compute

Principal Investigator:

Libo Chen

Affiliation:

Uppsala universitet

Start Date:

2025-08-22

End Date:

2026-09-01

Primary Classification:

10616: Molecular Biology

Webpage:

Allocation

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.