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. Author manuscript; available in PMC: 2007 Dec 10.
Published in final edited form as: Phys Rev E Stat Nonlin Soft Matter Phys. 2005 May 5;71(5 Pt 1):051902. doi: 10.1103/PhysRevE.71.051902

TABLE II.

Alternative Monte Carlo scheme for the dynamics of a single-stranded nucleic acid.

1 Generate a new lattice configuration for the polymer keeping the pin orientations fixed. That is, go through steps 1 to 5 in the algorithm described in Table I.
2 Thermalize the nucleotides in this new lattice configuration. That is, change the orientation of the pins following step 7 in the algorithm described in Table I.
3 Compute the energy of this new global configuration.
4 Accept or reject this new global configuration according to the METROPOLIS algorithm.