Non-equilibrium All-atom MD Simulations of Free and Tethered DNA molecules in Nano-channel Shear Flows <P>

I will talk about the new computational capability that we developed at NRL on the non-equilibrium molecular dynamics with biomolecules explicitly involved (BioNEMD).<P>

This capability was demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. Proper modeling of the surface and the surface linking was necessary and the obtained force field parameters were incorporated into the CHARMM database. Shear flows were generated and kept by translating the two surfaces in opposite directions.<P>

oth free and tethered DNA molecules are clearly observed to be stretching, rotating, and relaxing. Methods developed in this initial work can be incorporated into multiscale simulations including quantum mechanical, molecular and the microfluidic continuum regimes.