In-Silico-Single-Molecule-Manipulation-of-DNA-with-Rigid-Body-Dynamics-pcbi.1003456.s007

About

Illustration of the sampling efficiency of global versus local thermostat. This video records the simulated dynamics of a DNA molecule manipulated by magnetic tweezers after thermal equilibrium has been reached. The stretching force is pN and the number of turns of the bead is fixed to . From to s the simulation is run with Langevin local thermostat. Then the global thermostat is started up at s and run until s, strikingly accelerating the dynamics of the DNA molecule. Moreover the plectoneme starts to diffuse along the DNA molecule. Then the local thermostat is run again from s to , resulting in a dramatic slowing down of the dynamics. And finally the global thermostat is started up again at and run until the end of the video at . The DNA molecule is composed of rigid cylinders of radius and . The other parameters of the simulation are given in Table 1. This video is also available at http://vimeo.com/51918121.

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Wikimedia Commons, in Wikimedia Commons

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CC BY 4.0, as the Wikimedia Commons states it.

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Creative Commons Attribution 4.0

Credit

Carrivain P, Barbi M, Victor J

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