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A helicoidal transfer matrix model for inhomogeneous DNA melting

Tom Michoel·Yves Van de Peer
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Abstract

An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically stressed DNA with a fixed linking number constraint. Without loss of accuracy, the continuous degrees of freedom can be discretized using a minimal number of discretization points, yielding an effective transfer matrix model of modest dimension (d=36). The resulting algorithms to compute DNA melting profiles are both simple and efficient.

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Tom Michoel, Yves Van de Peer. 2006-10-13. A helicoidal transfer matrix model for inhomogeneous DNA melting. https://doi.org/10.1103/physreve.73.011908

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