Chain conformation of ring polymers under a cylindrical nanochannel confinement

Modulation of DNA conformation in electrolytic nanodroplets

The behavior of deoxyribonucleic acid (DNA) molecules in confinement is of profound importance in various bioengineering and medical applications. In the present study, all-atom molecular dynamics simulation is utilized to investigate the transition of the double-strand DNA (dsDNA) conformation in the electrolytic nanodroplet. Three typical conformations, i.e., C-shaped, folded S-shaped, and double C-shaped, are observed for different droplet sizes and ionic concentrations. To reveal the physics underlying this phenomenon, the characteristics of the dsDNA molecules, such as the overcharging intensity, the end-to-end distance, the radius of gyration, etc. are analyzed in detail based on the numerical results. It is found that the transition can be ascribed to the buckling of the polymer molecules under the compression due to the confinement of the nanodroplet, and it can be modulated by the ionic concentration in the electrolyte. Generally, nanoscale confinement dominates dsDNA behavior over the electrostatic effects in smaller nanodroplets, while the latter becomes more important for larger nanodroplets. This competition results in the persistence length increasing with the nanodroplet radii. Based on these discussions, a non-dimensional elasto-capillary number μ is proposed to classify the dsDNA conformations into three regions.

The polymer physics of single DNA confined in nanochannels

In recent years, applications and experimental studies of DNA in nanochannels have stimulated the investigation of the polymer physics of DNA in confinement. Recent advances in the physics of confined polymers, using DNA as a model polymer, have moved beyond the classic Odijk theory for the strong confinement, and the classic blob theory for the weak confinement. In this review, we present the current understanding of the behaviors of confined polymers while briefly reviewing classic theories. Three aspects of confined DNA are presented: static, dynamic, and topological properties. The relevant simulation methods are also summarized. In addition, comparisons of confined DNA with DNA under tension and DNA in semidilute solution are made to emphasize universal behaviors. Finally, an outlook of the possible future research for confined DNA is given.

Segregated structures of ring polymer melts near the surface: a molecular dynamics simulation study

We study structural properties of a ring polymeric melt confined in a film in comparison to a linear counterpart using molecular dynamics simulations. Local structure orderings of ring and linear polymers in the vicinity of the surface are similar to each other because the length scale of surface-monomer excluded volume interactions is smaller than the size of an ideal blob of the ring. In a long length scale, while the Silberberg hypothesis can be used to provide the physical origin of the confined linear polymer results, it no longer holds for the ring polymer case. We also present different structural properties of ring and linear polymers in a melt, including the size of polymers, the adsorbed amount, and the coordination number of a polymer. Our observation reveals that a confined ring in a melt adopts a highly segregated conformation due to a topological excluded volume repulsion, which may provide a new perspective to understand the nature of biological processes, such as territorial segregation of chromosomes in eukaryotic nuclei.

Effects of excluded volume and hydrodynamic interaction on the deformation, orientation and motion of ring polymers in shear flow

A ring polymer is a classical model to explore the behaviors of biomacromolecules. Compared with its linear counterpart in shear flow, the ring polymer should be more sensitive to excluded volume and hydrodynamic interaction attributed to the absence of chain ends. We carried out multiparticle collision dynamics combined with molecular dynamics simulation to study the effects of excluded volume and hydrodynamic interaction on the behaviors of ring polymers in shear flow. The results show that in the absence of the strong excluded volume interaction, the ring polymer prefers a two-strand linear conformation with high deformation and orientation in the flow-gradient plane, and the tank-treading motion is nearly negligible. Ring polymers without excluded volume show no significant difference from linear polymers in the scaling exponents for the deformation, orientation and tumbling motion. We also observed that the hydrodynamic interaction could efficiently slow down the relaxation of ring polymers while the scaling exponents against the Weissenberg number have rarely been affected.

Comparison of linear and ring DNA macromolecules moderately and strongly confined in nanochannels

Understanding the mechanism of DNA extension in nanochannels is necessary for interpretation of experiments in nanofluidic channel devices that have been conducted recently with both linear and ring chains. The present article reviews the situation with linear chains and analyses the experimental results and simulations for channel-induced extension (linearization) of ring chains. Results for confined rings indicate a transition between moderate and strong confinement similar to that of linear chains. Owing to stronger self-avoidance in confined rings, the transition and chain extension is shifted relative to linear DNA. We suggest that a relationship similar to that used for the extension of linear chains may also be used for circular DNA.