Nanopore

Molecular Dynamics Simulations of DNA
Electrophoresis through Nanopores

The following movies illustrate the MD simulations reported in the article. The thumbnail images are linked to the movies in MPEG 1 format. A short overview of the nanopore project can be found here.

Our latest MD simulations of DNA translocation through synthetic nanopores can be found here

Electrophoresis of DNA by strong electrical fields

Movie 1. Translocation of single stranded DNA through a nanopore in Si3N4.
Simulation conditions: Electrical field of 1.3x109 V/m generates a voltage bias of 21 V across the membrane; 1.3±0.1 nm diameter pore; 5.2 nm thick membrane; single stranded (dC)20, 1M solution of KCl; 40125 atoms simulated; total simulation time is 1.3 ns; NvT ensemble.


Electrophoresis of single stranded DNA
current and DNA CoM vs. timeOA
MPEG 1 (1.1 Mb)    

Movie 2. Translocation of double stranded DNA through a nanopore in Si3N4.
Simulation conditions: Electrical field 2.7x108 V/m corresponding to the voltage bias of 4.4 V; 2.4±0.2 nm diameter pore; 5.2nm thick membrane; double stranded (dC)20, 1M solution of KCl; 85207 atoms simulated; total simulation time is 3.7 ns; NvT ensemble.

Electrophoresis of single stranded DNA
current and DNA CoM vs. timeOA
MPEG 1 (2.2 Mb)    

Slow Electrophoresis of DNA

Movie 3. Slow electrophoresis of double stranded DNA through a nanopore in Si3N4.
Simulation conditions: Electrical field 8.7x107 V/m corresponding to the voltage bias of 1.4 V; 2.4±0.2 nm diameter pore; 5.2nm thick membrane; double stranded (dC)20, 1M solution of KCl; 85207 atoms simulated; total simulation time is  49.5 ns; NvT ensemble.

Electrophoresis of single stranded DNA
current and DNA CoM vs. timeOA
MPEG 1 (2.9 Mb)    


DNA--nanopore interaction

Movie 4. Spontaneous unzipping of the terminal DNA base pair inside a  Si3N4 nanopore.
Simulation conditions: Electrical field 8.7x106 V/m corresponding to the voltage bias of 0.14V; 2.4±0.2 nm diameter pore; 5.2nm thick membrane; double stranded (dC)20, 1M solution of KCl; 85207 atoms simulated; total simulation time  is 26 ns; NvT ensemble.

Electrophoresis of single stranded DNA
MPEG 1 (1.6 Mb)    


Blocking current without translocation

Movie 5. DNA it pulled sidewise inside the pore by an applied electrical field.
Simulation conditions: Electrical field 8.7x107 V/m corresponding to the voltage bias of 1.4 V; 2.4±0.2 nm diameter pore; 5.2nm thick membrane; double stranded (dC)20, 1M solution of KCl; 85207 atoms simulated; total simulation time  is 3 ns; NvT ensemble.
 
Electrophoresis of single stranded DNA
MPEG 1 (1.5 Mb)    


Movie 6. DNA it pulled sidewise inside the pore by a weak electrical field.
Simulation conditions: Electrical field 2.7x107 V/m corresponding to the voltage bias of 0.44 V; 2.4±0.2 nm diameter pore; 5.2 nm thick membrane; double stranded (dC)20, 1M solution of KCl; 85207 atoms simulated; total simulation time  is 4 ns; NvT ensemble.
 
Electrophoresis of single stranded DNA
MPEG 1 (1.8 Mb)