49 research outputs found
Hysteresis and nonequilibrium work theorem for DNA unzipping
We study by using Monte Carlo simulations the hysteresis in unzipping and
rezipping of a double stranded DNA (dsDNA) by pulling its strands in opposite
directions in the fixed force ensemble. The force is increased, at a constant
rate from an initial value to some maximum value that lies above
the phase boundary and then decreased back again to . We observed
hysteresis during a complete cycle of unzipping and rezipping. We obtained
probability distributions of work performed over a cycle of unzipping and
rezipping for various pulling rates. The mean of the distribution is found to
be close (the difference being within 10%, except for very fast pulling) to the
area of the hysteresis loop. We extract the equilibrium force versus separation
isotherm by using the work theorem on repeated non-equilibrium force
measurements. Our method is capable of reproducing the equilibrium and the
non-equilibrium force-separation isotherms for the spontaneous rezipping of
dsDNA.Comment: 8 figures, Final version to appear in Physical Review
Manipulating a single adsorbed DNA for a critical endpoint
We show the existence of a critical endpoint in the phase diagram of
unzipping of an adsorbed double-stranded (ds) polymer like DNA. The competition
of base pairing, adsorption and stretching by an external force leads to the
critical end point. From exact results, the location of the critical end point
is determined and its classical nature established.Comment: 6 pages, 5 figures, Published versio
Unzipping an adsorbed polymer in a dirty or random environment
The phase diagram of unzipping of an adsorbed directed polymer in two
dimensions in a random medium has been determined. Both the hard-wall and the
soft-wall cases are considered. Exact solutions for the pure problem with
different affinities on the two sides are given. The results obtained by the
numerical procedure adopted here are shown to agree with the exact results for
the pure case. The characteristic exponents for unzipping for the random
problem are different from the pure case. The distribution functions for the
unzipped length, first bubble, and the spacer are determined.Comment: Published version, uses revtex4, 14 page
Effects of Eye-phase in DNA unzipping
The onset of an "eye-phase" and its role during the DNA unzipping is studied
when a force is applied to the interior of the chain. The directionality of the
hydrogen bond introduced here shows oscillations in force-extension curve
similar to a "saw-tooth" kind of oscillations seen in the protein unfolding
experiments. The effects of intermediates (hairpins) and stacking energies on
the melting profile have also been discussed.Comment: RevTeX v4, 9 pages with 7 eps figure