Numerical simulation of the electrophoretic transport of a biopolymer through a synthetic nano-pore

Suresh Alapati, Dolfred Vijay Fernandes, Yong Kweon Suh

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)


We employed a hybrid approach to study numerically the translocation of a biopolymer through an artificial nano-pore driven by an external electric field in the presence of an explicit solvent. The motion of the polymer is simulated by the 3D Langevin dynamics technique. The hydrodynamic interactions (HI) between the polymer and the fluid are taken into account by the lattice Boltzmann equation. Our polymer chain model representing the double-stranded DNA was first validated by comparing the diffusion coefficient obtained from the numerical results with the experimental and theoretical results. Then, we conducted numerical simulations of the biopolymer's translocation process by applying a theoretical formula for the net electrophoretic force acting on the part of the polymer residing in the pore. We compared quantitatively the translocation times and the velocities of different DNA lengths with the corresponding experimental results. Our simulation results are in good agreement with the experimental ones when the HI are considered explicitly.

Original languageEnglish
Pages (from-to)466-477
Number of pages12
JournalMolecular Simulation
Issue number6
Publication statusPublished - 05-2011

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Information Systems
  • Modelling and Simulation
  • Chemical Engineering(all)
  • Materials Science(all)
  • Condensed Matter Physics


Dive into the research topics of 'Numerical simulation of the electrophoretic transport of a biopolymer through a synthetic nano-pore'. Together they form a unique fingerprint.

Cite this