Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: Excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models

摘要: We develop two classes of Monte Carlo moves for efficient sampling wormlike DNA chains that can have significant degrees supercoiling, a conformational feature is key to many aspects biological function including replication, transcription, and recombination. One class entails reversing the coordinates segment chain along one, two, or three axes an appropriately chosen local frame reference. These transformations may be viewed as generalization, continuum, Madras-Orlitsky-Shepp algorithm cubic lattices. Another moves, termed T+/-2, allows interconversions between with different lengths by adding subtracting beads (monomer units) from chain. Length-changing are generally useful given site juxtaposition, has been shown in previous lattice studies. Here, continuum T+/-2 designed enhance their acceptance rate supercoiled conformations. apply these model which excluded volume accounted bond-bond repulsion term. The computed autocorrelation functions relaxation bond length, angle, writhe, branch number indicate new lead significantly more than conventional bead displacements crankshaft rotations. A close correspondence found equilibrium ensemble map writhe pair segments juxtapositions self-contacts. To evaluate coarse-grained freely jointed (random-flight) models commonly used investigations, twisting (torsional) potentials introduced into models. Conformational properties superhelical density sigma then sampled computing using White's formula relate degree sigma. Extensive comparisons contact patterns knot probabilities show behaviors random-flight similar molecules solution environment high ionic strengths, whereas akin under low strengths.