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Molecular Dynamics Simulation of a Nanoscale Device for Fast Sequencing of DNA

Christina M. Payne, Chemical Engineering, Vanderbilt University, 24th and Garland Ave., 118 Olin Hall, Nashville, TN 37235, Xiongce Zhao, Nanomaterials Theory Institute, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, Peter T. Cummings, Chemical Engineering, Vanderbilt University and Oak Ridge National Laboratory, VU Station B, Box 351604, Nashville, TN 37235, and James W. Lee, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831.

A proposed novel nanotechnology concept which offers the possibility of unprecedented rapidity in the detection of DNA sequences is the focus of a multi-scale modeling study of transport and orientation properties of single strand DNA within a nanoscale channel. The proposed device consists of a detection gate of approximately two to five nanometers in width placed between two nonconductive plates. The DNA molecules in aqueous solution contained between the plates will be driven by an electric field through the detection gate. Individual base pairs within the DNA sequence are determined experimentally by examining the variations in the tunneling conductance of the gate. Electric fields are applied along both vertical and horizontal directions to control the motion of DNA segments and the orientations of the base pairs. Previous molecular dynamics simulations of the proposed device utilizing an inadequate metal/non-metal interaction potential have prompted the examination of an alternative implementation of charge dynamics to properly represent the interactions. Additionally, an alternative to the use of an electric field as a controlling mechanism is examined. Results from these molecular dynamics simulations are presented. Ideally, results from these molecular dynamics simulations and ab initio calculations of differences in tunneling electron transport across the nanoscale gap as different amino acids pass through the gap will be combined with the experimental fabrication of the actual device. Both the computational and experimental projects are supported by complementary NIH grants.