Bubble Formation in Helicoidal DNA Molecules
نویسندگان
چکیده
منابع مشابه
Bubble propagation in a helicoidal molecular chain.
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the "transcription bubble," where the hydrogen bonds between complementary bases are disrupted, allowing access to the genetic code. We propose these kinds of excitations in alternative to kinks and breathers. The model...
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Z. Rapti, A. Smerzi, K. Ø. Rasmussen and A. R. Bishop 1 Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and School of Mathematics, Institute for Advanced Study, Einstein Drive 1, Princeton, New Jersey 08540 2 Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 and 3 Istituto Nazionale di ...
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Maria Barbi, Simona Cocco and Michel Peyrard 1 Istituto Nazionale di Fisica Nucleare, Dipartimento di Fisica, Universitá degli Studi di Firenze, Largo E. Fermi, 2 50125 Firenze, Italy 2 Dipartimento di Scienze Biochimiche Universitá di Roma ”La Sapienza” P.le A. Moro, 5 00185 Roma, Italy 3 Laboratoire de Physique, CNRS URA 1325, Ecole Normale Supérieure de Lyon, 46 Allée d’Italie, 69364 Lyon Ce...
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Abstract The thermodynamical stability of a set of circular double helical molecules is analyzed by path integral techniques. The minicircles differ only in i) the radius and ii) the number of base pairs (N) arranged along the molecule axis. Instead, the rise distance is kept constant. For any molecule size, the computational method simulates a broad ensemble of possible helicoidal configuratio...
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The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path integral techniques, simulates a distribution of topoisomers with various twist numbers and finds the energetically most favorable molecular conformation as ...
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ژورنال
عنوان ژورنال: Journal of Physical Chemistry & Biophysics
سال: 2016
ISSN: 2161-0398
DOI: 10.4172/2161-0398.1000230