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Subject: search.filters.subject.DNA Chain

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    Role of chain stiffness and end entropy in the unzipping of DNA chain
    (AIP, 2013-06) Singh, Navin
    The force induced unzipping of dsDNA was studied in Constant Force Ensembles (CFE) in presence of salt. The role of end entropy on the force required to unzip the chain has been investigated using Peyrard Bishop Dauxious (PBD) model. The effect of the stiffness and anharmonicity in the stacking interaction of the chain has been investigated. Our results show that the force require to unzip the chain increases with increasing the chain length in case when the other end is free while it decreases in case of when the other end of the chain is restricted. However, as the chain length reaches a critical length, the end effect nullifies and the critical force in both the cases are found to be same.
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    Statistical mechanics of thermal denaturation of DNA oligomers
    (Springer, 2003-08) Singh, Navin
    Double stranded DNA chain is known to have non-trivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state. The effect of this constraint on the denaturation profile of the oligomer has been calculated using the Peyrard-Bishop Hamiltonian. The denaturation profile is found to be very different from the free (i.e. without the constraint) oligomer. We have also examined how this constraint affects the denaturation profile of the oligomer having a segment of defect sites located at different parts of the chain.
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    Pulling DNA: The Effect of Chain Length on the Mechanical Stability of DNA Chain
    (Wiley, 2015-11) Singh, Navin
    We have investigated the effect of chain length on the thermal denaturation as well as on mechanical unzipping of double stranded DNA (ds-DNA) molecule. We use a simple nonlinear Peyrard Bishop and Dauxois (PBD) model and calculate the melting temperature as well as the critical force as a function of chain length for different heterogeneous chains. We found that in mechanical unzipping, when a force is applied on an end, there is a length up-to which the effect of applied force sustains. The base pairs beyond this length can not feel the force that is applied on the end. We have studied the chain with other end to be open and with the other end to be restricted. By comparing the force required to unzip the chain in these two cases, we found a critical length above which the entropy contribution from the end is not significant to change the duplex state of the chain. For shorter chain, we found that the entropic forces due to open end have significant contribution to change the duplex state of DNA to single strand state of DNA chain.