  We characterize the pH controlled polymer capture and transport thorough
silicon nitride (SiN) pores subject to protonation. A charge regulation model
able to reproduce the experimental zeta potential of SiN pores is coupled with
electrohydrodynamic polymer transport equations. The formalism can
quantitatively explain the experimentally observed non-monotonic pH dependence
of avidin conductivity in terms of the interplay between the electroosmotic and
electrophoretic drag forces on the protein. We also scrutinize the DNA
conductivity of SiN pores. We show that in the low pH regime where the
amphoteric pore is cationic, DNA-pore attraction acts as an electrostatic trap.
This provides a favorable condition for fast polymer capture and extended
translocation required for accurate polymer sequencing.
