A helicoidal transfer matrix model for inhomogeneous DNA melting
arXiv:q-bio/0507036 · doi:10.1103/PhysRevE.73.011908
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.
v3: Matlab toolbox included with source file; article unchanged, 12 pages, 11 figures, RevTeX
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