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. Author manuscript; available in PMC: 2015 Oct 15.
Published in final edited form as: J Phys Condens Matter. 2014 Sep 19;26(41):413101. doi: 10.1088/0953-8984/26/41/413101

Figure 14.

Figure 14

MD simulation of the effective force on DNA in a nanopore. (a) Simulation setup. Two strands of DNA are colored in purple and blue; K+ (tan) and Cl− (cyan) ions are shown as spheres; water (green) is shown as a semitransparent surface. A mechanical tether force is applied to the DNA via a harmonic potential (a virtual spring). One end of the spring is fixed in space whereas the other end is attached to the center of mass of the DNA fragment. A uniform external electric field E is applied to the whole system. The DNA molecule is made effectively infinite by connecting the backbone to its image across the periodic boundary. (b) The restraining force versus the simulation time for several values of the applied electric field. The color of the lines corresponds to the color of the symbols in panel c. (c) The average effective force acting on DNA versus the nominal force of the electrostatic field QE, where Q is the nominal electrical charge of DNA. Figures were adapted from Ref. 316 with permission. Copyright 2008 by the American Physical Society.