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Dna Cyclization And Looping In The Wormlike Limit: Normal Modes And The Validity Of The Harmonic Approximation, Stefan M. Giovan, Andreas Hanke, Stephen D. Levene

Physics and Astronomy Faculty Publications and Presentations

For much of the last three decades, Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, J, or J factor, for DNA models having sequence-dependent bends or inhomogeneous bending flexibility. Within the last 10 years approaches based on harmonic analysis of semi-flexible polymer models have been introduced, which offer much greater computational efficiency than Monte Carlo techniques. These methods consider the ensemble of molecular conformations in terms of harmonic fluctuations about a well-defined elastic-energy minimum. However, the harmonic approximation is only applicable for small systems, because the accessible conformation space of larger systems is increasingly …