Towards an MD simulation of ion currents in the alpha hemolysin channel

Experiments show that single stranded nucleic acids polymers can be transported across an alpha hemolysin channel under the action of an applied electric field. The translocation of the nucleic acid polymers causes transient blockades in the ion current. The physical and chemical details of the interactions between polymer, channel and ionic solution that lead to the blockade events are not yet fully understood. Atomistic simulations enable a realistic description of the dynamic motions of the solvated polymer-pore system as a function of time. Analysis of such calculated system trajectories leads to valuable insight possible energy barriers, ion mobilities and short time-scale interactions. This study investigates the relationship between the structural properties of the alpha hemolysin channel and the ionic current blockades that result from the translocation of single stranded nucleic acids.