Search results for "Persistence length"

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 …

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 …

Computer Simulations for Polymer Dynamics

1991

In this paper we review recent work on the dynamics of polymeric systems using computer simulation methods. For a two-dimensional polymer melt, we show that the chains segregate and the dynamics can be described very well by the Rouse model. This simulation was carried out using the bond fluctuation Monte Carlo method. For three-dimensional (3d) melts and for the study of hydrodynamic effects, we use a molecular dynamics simulation. For 3d melts our results strongly support the concept of reptation. A detailed comparison to experiment shows that we can predict the time and length scales for the onset of reptation for a variety of polymeric liquids. For a single chain, we find the expected h…

Capillary Nematization of Semiflexible Polymers

2016

emiflexible polymers under good solvent conditions confined by two planar parallel repulsive walls are investigated for a wide range of monomer concentrations and distances between the walls, for a case where persistence length and contour length of the macromolecules are almost equal. Chain conformations and local nematic ordering near the walls are studied by both molecular dynamics methods and density functional theory, putting it in perspective with the recent work where the isotropic phase of semiflexible polymer solutions in the vicinity of a single repulsive wall in semi-infinite geometry is considered. Profiles of the total density of monomers as well as densities of end- and middle…

Densely packed semiflexible macromolecules in a rigid spherical capsule

2018

The ordering of semiflexible polymers with persistence length lp and contour length L confined in a sphere of radius R is studied by molecular dynamics simulations of a coarse-grained model. Monomer densities are chosen where the corresponding bulk lyotropic solution or melt is a well-ordered nematic, and purely repulsive walls of the rigid confining sphere are considered. It is found that polymers close to the walls are bent according to the curvature of the confining spheres with all their monomers in a few layers parallel to the sphere surface, whereas the remaining macromolecules closer to the sphere center have one chain end and their center of mass far from the surface. The latter cha…

Semiflexible Polymers in the Bulk and Confined by Planar Walls

2016

Semiflexible polymers in solution under good solvent conditions can undergo an isotropic-nematic transition. This transition is reminiscent of the well-known entropically-driven transition of hard rods described by Onsager’s theory, but the flexibility of the macromolecules causes specific differences in behavior, such as anomalous long wavelength fluctuations in the ordered phase, which can be understood by the concept of the deflection length. A brief review of the recent progress in the understanding of these problems is given, summarizing results obtained by large-scale molecular dynamics simulations and density functional theory. These results include also the interaction of semiflexib…

Self-assembly of semiflexible polymers confined to thin spherical shells

2018

Confinement effects are critical for stiff macromolecules in biological cells, vesicles, and other systems in soft matter. For these molecules, the competition between the packing entropy and the enthalpic cost of bending is further shaped by strong confinement effects. Through coarse-grained molecular dynamics simulations, we explore the self-assembly of semiflexible polymers confined in thin spherical shells for various chain lengths, chain stiffnesses, and shell thicknesses. Here, we focus on the case where the contour and persistence length of the polymers are comparable to the radius of the confining cavity. The range of ordered structures is analyzed using several order parameters to …

Flexibility of phenylene oligomers revealed by single molecule spectroscopy

2006

The rigidity of a p-phenylene oligomer (p-terphenyl) has been investigated by single molecule confocal fluorescence microscopy. Two different rylene diimide dyes attached to the terminal positions of the oligomer allowed for wavelength selective excitation of the two chromophores. In combination with polarization modulation the spatial orientation of the transition dipoles of both end groups could be determined independently. We have analyzed 597 single molecules in two different polymer hosts, polymethylmethacrylate and Zeonex. On average we find a 22 degrees deviation from the linear gas phase geometry (T = 0 K), indicating a rather high flexibility of the p-phenylene oligomer independent…

Semi-flexible polymer chains in quasi-one-dimensional confinement: a Monte Carlo study on the square lattice

2013

Single semi-flexible polymer chains are modeled as self-avoiding walks (SAWs) on the square lattice with every 90° kink requiring an energy eb. While for eb = 0 this is the ordinary SAW, varying the parameter qb = exp(−eb/kBT) allows the variation of the effective persistence length p over about two decades. Using the pruned-enriched Rosenbluth method (PERM), chain lengths up to about N = 105 steps can be studied. In previous work it has already been shown that for contour lengths L = Nb (the bond length b is the lattice spacing) of order p a smooth crossover from rods to two-dimensional self-avoiding walks occurs, with radii R ∝ p1/4L3/4, the Gaussian regime predicted by the Kratky–Porod m…

Semiflexible polymers confined in a slit pore with attractive walls: two-dimensional liquid crystalline order versus capillary nematization

2017

Semiflexible polymers under good solvent conditions interacting with attractive planar surfaces are investigated by Molecular Dynamics (MD) simulations and classical Density Functional Theory (DFT). A bead-spring type potential complemented by a bending potential is used, allowing variation of chain stiffness from completely flexible coils to rod-like polymers whose persistence length by far exceeds their contour length. Solvent is only implicitly included, monomer-monomer interactions being purely repulsive, while two types of attractive wall-monomer interactions are considered: (i) a strongly attractive Mie-type potential, appropriate for a strictly structureless wall, and (ii) a corrugat…