0000000000682377
AUTHOR
Florian C. Rieger
showing 4 related works from this author
Coarse-grained models of double-stranded DNA based on experimentally determined knotting probabilities
2018
Abstract To accurately model double-stranded DNA in a manner that is computationally efficient, coarse-grained models of DNA are introduced, where model parameters are selected by fitting the spectrum of observable DNA knots: We develop a general method to fit free parameters of coarse-grained chain models by comparing experimentally obtained knotting probabilities of short DNA chains to knotting probabilities that are computed in Monte Carlo simulations, resulting in coarse-grained DNA models which are tailored to reflect DNA topology in the best possible way. The method is exemplified by fitting ideal chain models as well as a bead-spring model with excluded volume interactions, to model …
Influence of chain stiffness on knottedness in single polymers.
2013
In the present article, we investigate and review the influence of chain stiffness on self-entanglements and knots in a single polymer chain with Monte Carlo simulations spanning good solvent, theta and globular phases. The last-named are of particular importance as a model system for DNA in viral capsids. Intriguingly, the dependence of knot occurrence and complexity with increasing stiffness is non-trivial, but can be understood with a few simple concepts outlined in the present article.
Entropic Interactions between Two Knots on a Semiflexible Polymer.
2017
Two knots on a string can either be separated or intertwined, and may even pass through each other. At the microscopic scale, such transitions may occur spontaneously, driven by thermal fluctuations, and can be associated with a topological free energy barrier. In this manuscript, we study the respective location of a trefoil ( 3 1 ) and a figure-eight ( 4 1 ) knot on a semiflexible polymer, which is parameterized to model dsDNA in physiological conditions. Two cases are considered: first, end monomers are grafted to two confining walls of varying distance. Free energy profiles and transition barriers are then compared to a subset of free chains, which contain exactly one 3 1 and one 4 1 kn…
A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains.
2016
We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on …