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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 10.

Figure 10

SMD simulation of nucleosomal DNA unwrapping. (a–e) Representative conformations of a partially unwrapped nucleosome at several instances of the SMD trajectory. To realize the SMD protocol, a harmonic spring potential was applied between the centers of mass of the terminal fragments (10 bp) of DNA. The equilibrium length of the spring was increased at a rate of v to unwrap the nucleosome. The inset in panel e illustrates local melting of DNA produced by the excessive SMD force (~100 pN). (f) SMD force as a function of the simulation time. Note that the pulling rate was reduced by a factor of 5 at t ~ 18 ns to facilitate structural relaxation.