  We report a novel simulation strategy that enables us to identify key
parameters controlling the experimentally measurable characteristics of
structural protein tags on dsDNA construct translocating through a double
nanopore setup. First, we validate the scheme in silico by reproducing and
explaining the physical origin of the experimental dwell time distributions of
the Streptavidin markers on a 48 kbp long dsDNA. These studies reveal the
important differences in the characteristics of the protein tags compared to
the dynamics of dsDNA segments, immediately providing clues on how to improve
the measurement protocols to decipher the unknown genomic lengths accurately.
Of particular importance is the in silico studies on the effect of electric
field inside and beyond the pores which we find is critical to discriminate
protein tags based on their effective charges and masses revealed through a
generic power-law dependence of the average dwell time at each pore. The
simulation protocols enable to monitor piecewise dynamics of the individual
monomers at a sub-nanometer length scale and provide an explanation of the
disparate velocity variation from one tag to the other using the nonequilibrium
tension propagation theory, - a key element to decipher genomic lengths
accurately. We further justify the model and the chosen simulation parameters
by calculating the Peclet number which is in close agreement with the
experiment. Analysis of our simulation results from the CG model has the
capability to refine the accuracy of the experimentally obtained genomic
lengths and carefully chosen simulation strategies can serve as a powerful tool
to discriminate different types of neutral and charged tags of different
origins on a dsDNA construct in terms of their physical characteristics and can
provide insights to increase both the efficiency and accuracy of an
experimental dual-nanopore setup.
