1999/03/24 by Boris Fain, Joseph Rudnick
Biochemistry, Genetics and Molecular Biology · Environmental Science · Mathematics · Physics and Astronomy · #Bacteriophages and microbial interactions #Biology #Classical mechanics #Computer science #Constraint (computer-aided design) #DNA #DNA and Nucleic Acid Chemistry #Energy (signal processing) #Genetics #Geometry #Mathematics #Physics #Quantum mechanics #RNA and protein synthesis mechanisms #Stability (learning theory) #Theoretical physics #cond-mat.soft #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.1103/physreve.60.7239
39 pages in REVTEX with 14 eps figures. Submitted to Phys. Rev. E. This manuscript updates, expands and revises, to a considerable extent, a previously posted manuscript, entitled "Conformations of Circular DNA," which appeared as cond-mat/9701040
arxiv created 1999/03/24 · openalex publication_date 1999/12/01 · arxiv updated 2009/11/30 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic expressions leading to the spatial configuration of a family of solutions representing distortions that interpolate between the circular form of DNA and a figure-eight form that represents the onset of interwinding. We are also able to generate knotted loops. We suggest ways to use our approach to produce other configurations relevant to studies of DNA structure. The stability of the distorted configurations is assessed, along with the effects of fluctuations on the free energy of the various configurations.