Finite element analysis of DNA supercoiling

Yang Yang, Irwin Tobias, Wilma K. Olson

Research output: Contribution to journalArticlepeer-review

85 Scopus citations


A DNA polymer with hundreds or thousands of base pairs is modeled as a thin elastic rod. To find the equilibrium configurations and associated elastic energies as a function of linking number difference (ΔLk), a finite element scheme based on Kirchhoff's rod theory is newly formulated so as to be able to treat self-contact. The numerical results obtained here agree well with those already published, both analytical and numerical, but a much more detailed picture emerges of the several equilibrium states which can exist for a given ΔLk. Of particular interest is the discovery of interwound states having odd integral values of the writhing number and very small twist energy. The existence of a noncircular cross section, inhomogeneous elastic constants, intrinsic curvature, and sequence-dependent bending and twisting can all be readily incorporated into the new formalism.

Original languageEnglish (US)
Pages (from-to)1673-1686
Number of pages14
JournalThe Journal of Chemical Physics
Issue number2
StatePublished - 1993

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry


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