Dresden 2026 – scientific programme

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BP: Fachverband Biologische Physik

BP 2: Computational Biophysics I

BP 2.9: Talk

Monday, March 9, 2026, 11:45–12:00, BAR/0106

Protein Translocation in Two Dimensional Nanopores from Molecular Dynamics and Free Energy Calculations — •Peijia Wei, Mayukh Kansari, Santiago López Páramo, and Maria Fyta — Computational Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany

Nanopores, nanometer scale openings in materials, offer strong potential for ultra fast, cost effective and real time next generation sequencing technologies. These pores can electrophoretically drive charged biomolecules through and detect them. Using computer simulations, we compare two dimensional nanopores, graphene and MoS₂, to evaluate their effectiveness in protein detection. Protein translocation and dynamics are being controlled by varying the surrounding solvent, using both a typical monovalent salt solution and a molecular solution. Atomistic simulations assess the ability of each nanopore to thread proteins, on the basis of the ionic current signals through the pore. We also perform free energy calculations to quantify the thermodynamic factors that influence protein entry and passage through the pores. Our results show that graphene nanopores interact strongly with proteins, which hinders translocation under physiological conditions. This can be overcome by adding a denaturant that forms a hydrophilic and cation rich layer on the surface and enables linearized threading. In contrast, MoS₂ nanopores allow protein passage even in physiological solutions and offer inherent control of the translocation. By combining molecular dynamics with free energy analysis, we reveal how the complex interactions among all components shape translocation behavior.

Keywords: Molecular Dynamics simulation; Solid-state nanopore; Protein detection; Free energy