Helicoidal transfer matrix model for inhomogeneous DNA melting

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jan;73(1 Pt 1):011908. doi: 10.1103/PhysRevE.73.011908. Epub 2006 Jan 13.

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.