Unzipping DNA by force: thermodynamics and finite size behaviour

Abstract

We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size scaling of thermodynamic quantities like the extensibility, the length of the unzipped segment of a Y-fork, the phase diagram can be recovered. We suggest that such procedures could be used to obtain the thermodynamic phase diagram from experiments on finite length DNA.

Can a double stranded DNA be unzipped by pulling a single strand?: Phases of adsorbed DNA

“…By using the Bhattacharjee-Seno procedure, we obtained d = 2.02 ± 0.01, φ = 1.01±0.01 with g u = 2.692±0.001. These exponents are same as the exponents for the DNA unzipping by pulling strands in the opposite directions [4,6,10]. This indicates that, similar to the later case, the unzipping by pulling a single strand is also a first order phase transition with…”

“…The 2N such flips, N for each strand, constitutes one Monte Carlo step (MCS) per bead. At each value of the force, where the simulation is performed, we allow the system to equilibrate by repeating the above procedure for 10 6 MCS and start measurements only after it. Between any two measurements we run the procedure, without doing measurements, for 10 3 MCS to avoid correlations between two measurements.…”

Hysteresis loop area scaling exponents in DNA unzipping by a periodic force: A Langevin dynamics simulation study

“…In this paper, we study the unzipping transition of a ds-DNA subjected to a periodic force using LD simulations on a model that is very much similar to a well established DSAW model of a DNA on a D = 1 + 1 square lattice. The later model has been studied extensively, for over two decades, using the generating function, exact transfer matrix, and Monte Carlo techniques [1,2,[7][8][9][25][26][27][28][29]. Furthermore, the length of the DNA, having up to 184 monomers with N = 96 base pairs, simulated here, for the periodic case, are six times longer than the earlier BD/LD simulation studies [20][21][22][23][24].…”

Strong Coupling and Nonextensive Thermodynamics

“…Small-sized systems, such as single molecules [ 2 ], atomic clusters [ 3 ], biopolymers [ 4 ], molecular motors [ 5 ], or nanoporous membranes [ 6 , 7 ], are typical examples of nonextensive systems. The energy, mass, and volume of these systems can be significantly altered by what is around them, and their scale related properties often escape the paradigms of classical thermodynamics [ 8 ].…”