Paper Citing NAMD - Abstract
Cozmuta, I.; O'Keeffe, J.T.; Stolc, V.
Hybrid MD-PNP simulations of the alpha-hemolysin open channel ionic current
NSTI NANOTECH 2004, VOL 1, TECHNICAL PROCEEDINGS, 143-146, 2004
Experiments have shown that single stranded nucleic acids polymers can be transported through the alpha-hemolysin ion channel under the action of an applied electric field. The translocation of the nucleic acid polymers causes transient blockade of the ionic current. The physical and chemical details of the interactions between polymer, channel and ionic solution that control the blockade events are not yet fully understood. To study such interactions, a hybrid MD-PNP model is proposed. The diffusion coefficient of the ions (0.78(.)10(-9) m(2)/s) and pore wall charges are determined from MD simulations. These values are used in the PNP model to calculate open channel ionic currents. The calculated value for ionic current (101 pA) is close to the experimental value (120 pA) only when pore-wall charges are included in the model in addition to the pore geometry. This validates the present approach of bridging time scales by combining a microscopic and macroscopic model.
