Paper Citing NAMD - Abstract
Luan, Binquan; Aksimentiev, Aleksei
Electro-osmotic screening of the DNA charge in a nanopore
PHYSICAL REVIEW E, 78 Art. No. 021912, AUG 2008
Extensive all-atom molecular dynamics simulations were performed to characterize the microscopic origin of the force experienced by DNA in a bulk electrolyte and a solid-state nanopore when subject to ail external electrostatic field E. The effective screening of the DNA charge was found to originate from the hydrodynamic drag of the electro-osmotic flow that is driven by the motion of counterions along the surface of DNA. We show that the effective driving force F in a nanopore obeys the same law as in a bulk electrolyte: F=xi mu E, where xi and mu are the friction coefficient and electrophoretic mobility of DNA, respectively. Using this relationship, we suggest a method for determining the effective driving force on DNA in a nanopore that does not require a direct force measurement.
