Mesoscopic model for nano-channel confined DNA
arXiv:1909.03202 · doi:10.1088/1742-6596/1391/1/012004
Abstract
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations. It is shown that, for the specific case of a short DNA fragment in a nanochannel, the molecule is markedly over-twisted and stretched by narrowing the width of the channel.
8th International Conference on Mathematical Modeling in Physical Sciences. August 26-29, 2019 - Bratislava, Slovakia
References in corpus (10)
- Path Integral Method for DNA Denaturation
- Denaturation Patterns in Heterogeneous DNA
- Stacking Interactions in Denaturation of DNA Fragments
- J-factors of short DNA molecules
- End-to-end distance and contour length distribution functions of DNA helices
- Flexibility of short DNA helices under mechanical stretching
- Twisting and Bending Stress in DNA Minicircles
- Entropic Penalties in Circular DNA Assembly
- Twisting short dsDNA with applied tension
- Short DNA persistence length in a mesoscopic helical model