The team used high-performance supercomputers to predict the change in conductance of silicon nitride nanopores during the brief moments that proteins occupy the pore during translocation. For a pore that had an hourglass profile, they found that the conductance was sensitive to the position of the protein, with a smaller drop in conductance if the protein was placed at the pore entrance instead of its centre. For high concentrations of proteins, situations might arise where more than one protein occupies the nanopore at a time. This was also considered in the calculations with the result that the change in conductance does not quite scale linearly with the number of proteins within the pore, instead it is a complex function of their position.

Time dependence

Time-dependent properties of the translocation process were also considered by performing steered molecular dynamics simulations to guide proteins through the pore at a rate accessible to computational methods. From this the variation in the drag coefficient of the protein due to the confined geometry of the pore could be monitored.

Taken together, the results from the position-dependent and the steered simulations help give molecular-level insight into the two key quantities that experimental researchers commonly use to characterize the translocation process: the magnitude of the current drop and its duration.

More information can be found in the journal Nanotechnology 25 155502.

Further reading

Passivated nanopores withstand extreme voltages (July 2011)
Probing an individual DNA molecule thousands of times with a nanopore (Oct 2013)
Nanopores form more quickly through FIB boiling (Jan 2014)