Faculty
Science
Supervisor Name
Colin Denniston
Keywords
polymer translocation, solid-state pore, nanopore, LAMMPS, lattice-Boltzmann
Description
Solid-state nanopore sensors remain a promising solution to the rising global demand for genome sequencing. These single-molecule sensing technologies require single-file translocation for high resolution and accurate detection. This study uses molecular dynamics-lattice Boltzmann simulations of the capture of a single polymer chain under pressure-driven hydrodynamic flow to investigate a method of increasing the single-file capture and translocation rate. By using a model force of two oppositely electrically charged rings, single-file capture in hydrodynamic flow can be amplified from about 45% to 51.5%. This paper found that the optimal values of force location, force strength, and system pressure/flow velocity are neither too high nor too low and are roughly parabolic in shape near the apex. Thus, implementing an electrical force and optimizing these variables can result in a higher probability of threading a polymer through a nanopore in a single-file fashion.
Acknowledgements
I would like to thank my supervisor, Professor Colin Denniston for allowing me to work with his research team on this project and for his guidance throughout its production. I would also like to thank my supervising graduate student, Navid Afrasiabian, for all his time, effort, teaching, and guidance throughout this project. Finally, thank you to the Western USRI team and program for making this research opportunity possible.
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License
Document Type
Paper
Polymer translocation through a nanopore: Controlling capture conformations using an electrical force
Solid-state nanopore sensors remain a promising solution to the rising global demand for genome sequencing. These single-molecule sensing technologies require single-file translocation for high resolution and accurate detection. This study uses molecular dynamics-lattice Boltzmann simulations of the capture of a single polymer chain under pressure-driven hydrodynamic flow to investigate a method of increasing the single-file capture and translocation rate. By using a model force of two oppositely electrically charged rings, single-file capture in hydrodynamic flow can be amplified from about 45% to 51.5%. This paper found that the optimal values of force location, force strength, and system pressure/flow velocity are neither too high nor too low and are roughly parabolic in shape near the apex. Thus, implementing an electrical force and optimizing these variables can result in a higher probability of threading a polymer through a nanopore in a single-file fashion.