dorsal/arxiv
View SchemaTorsional fluctuations in columnar DNA assemblies
| Authors | D. J. Lee, A. Wynveen |
|---|---|
| Categories | |
| ArXiv ID | physics/0511009 |
| URL | https://arxiv.org/abs/physics/0511009 |
| DOI | 10.1088/0953-8984/18/3/004 |
Abstract
In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy between neighbouring molecules explicitly depends on their relative azimuthal orientations. For DNA this leads to a rich variety of mesophases for columnar assemblies, each categorized by a specific azimuthal ordering. In a preceding paper [A. Wynveen, D. J. Lee, and A. A. Kornyshev, Eur. Phys. J. E, 16, 303 (2005)] a statistical mechanical theory was developed for the assemblies of torsionally rigid molecues in order to determine how thermal fluctuations influence the structure of these mesophases. Here we extend this theory by including torsional fluctuations of the molecules, where a DNA molecule may twist about its long axis at the cost of torsional elastic energy. Comparing this with the previous study, we find that inclusion of torsional fluctuations further increases the density at which the transition between the hexagonal structure and the predicted rhombic phase occurs and reduces the level of distortion in the rhombic phase. As X-ray diffraction may probe the 2-D lattice structure of such assemblies and provide information concerning the underlying interaction between molecules, we have also calculated correlation functions for the azimuthal ordering which are manifest in an x-ray scattering intensity profiles.
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"abstract": "In columnar assemblies of helical bio-molecules the azimuthal degrees of\nfreedom, i.e. rotations about the long axes of molecules, may be important in\ndetermining the structure of the assemblies especially when the interaction\nenergy between neighbouring molecules explicitly depends on their relative\nazimuthal orientations. For DNA this leads to a rich variety of mesophases for\ncolumnar assemblies, each categorized by a specific azimuthal ordering. In a\npreceding paper [A. Wynveen, D. J. Lee, and A. A. Kornyshev, Eur. Phys. J. E,\n16, 303 (2005)] a statistical mechanical theory was developed for the\nassemblies of torsionally rigid molecues in order to determine how thermal\nfluctuations influence the structure of these mesophases. Here we extend this\ntheory by including torsional fluctuations of the molecules, where a DNA\nmolecule may twist about its long axis at the cost of torsional elastic energy.\nComparing this with the previous study, we find that inclusion of torsional\nfluctuations further increases the density at which the transition between the\nhexagonal structure and the predicted rhombic phase occurs and reduces the\nlevel of distortion in the rhombic phase. As X-ray diffraction may probe the\n2-D lattice structure of such assemblies and provide information concerning the\nunderlying interaction between molecules, we have also calculated correlation\nfunctions for the azimuthal ordering which are manifest in an x-ray scattering\nintensity profiles.",
"arxiv_id": "physics/0511009",
"authors": [
"D. J. Lee",
"A. Wynveen"
],
"categories": [
"physics.bio-ph"
],
"doi": "10.1088/0953-8984/18/3/004",
"title": "Torsional fluctuations in columnar DNA assemblies",
"url": "https://arxiv.org/abs/physics/0511009"
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