Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties
arXiv:1204.1983 · doi:10.1021/ma202503k
Abstract
Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 m range and slits widths spanning continuously the 50--1250nm range. The metric scaling predicted by de Gennes' blob model is shown to hold for both linear and circularised DNA up to the strongest levels of confinement. More notably, the topological properties of the circularised DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is non-monotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Secondly, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nano-slits could be used in nano-fluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type.
12 pages, 10 figures
References in corpus (19)
- Physical approaches to DNA sequencing and detection
- Polymers with spatial or topological constraints: theoretical and computational results
- Accurate estimate of the critical exponent for self-avoiding walks via a fast implementation of the pivot algorithm
- Scaling theory of DNA confined in nanochannels and nanoslits
- Critical exponents for random knots
- Probing the entanglement and locating knots in ring polymers: a comparative study of different arc closure schemes
- Scaling exponents and probability distributions of DNA end-to-end distance
- What is the length of a knot in a polymer?
- Fractal Dimension and Localization of DNA Knots
- Topologically Driven Swelling of a Polymer Loop
- Knotting of random ring polymers in confined spaces
- Knot-controlled ejection of a polymer from a virus capsid
- Conformation of Circular DNA in 2 Dimensions
- Multiscale entanglement in ring polymers under spherical confinement
- Structure and dynamics of ring polymers: entanglement effects because of solution density and ring topology
- Confinement of knotted polymers in a slit
- Universal properties of a single polymer chain in slit: Scaling versus MD simulations
- Characteristic length of random knotting for cylindrical self-avoiding polygons
- Excluded volume effects on semiflexible ring polymers
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- The circular Kardar-Parisi-Zhang equation as an inflating, self-avoiding ring polymer
- Hydrodynamic Effects on Confined Polymers
- Machine learning understands knotted polymers
- On the factorization of composite polymer knots into separated prime components
- The Shape of a Stretched Polymer
- Ring polymers in confined geometries
- The free energy of compressed lattice knots
- Variational autoencoders understand knot topology
- Proteins analysed as virtual knots
- Knotting and weak knotting in confined, open random walks using virtual knots
- Knotting of linear DNA in nano-slits and nano-channels: a numerical study
- Hydrodynamic Inflation of Ring Polymers under Shear