Monte Carlo study of force induced melting of DNA hairpin

Thermodynamic properties of a DNA hairpin are investigated employing non-Boltzmann Monte Carlo simulation. We model the DNA hairpin as a polymer on a two dimensional square lattice. We Consider bond fluctuation model with each bead occupying four-sites. The system exhibits a transition from a closed...

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Bibliographic Details
Published in:Physica A 2015-06, Vol.428, p.38-45
Main Authors: Suman Kalyan, M., Murthy, K.P.N.
Format: Article
Language:English
Subjects:
Bond fluctuation method
DNA
Monte Carlo
Phase transition
Thermodynamics
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Summary:Thermodynamic properties of a DNA hairpin are investigated employing non-Boltzmann Monte Carlo simulation. We model the DNA hairpin as a polymer on a two dimensional square lattice. We Consider bond fluctuation model with each bead occupying four-sites. The system exhibits a transition from a closed loop phase to a open phase. This can be induced by increasing temperature and is called melting. We investigate the effect of force on melting transition by calculating free energy. We report results on force–temperature phase diagram. From free energy curves we observe that the phase transition is discontinuous. We also present results on average energy, average extension and heat capacity as a function of temperature. •Successfully employed Bond fluctuation method to lattice model of hp-DNA.•Force–temperature phase diagram obtained.•Calculated free energy profile to show transition is discontinuous.
ISSN:0378-4371
1873-2119
DOI:10.1016/j.physa.2015.02.036