Related papers: Entropic alignment of topologically modified ring …
The number of allowed configurations of a polymer is reduced by the presence of a repulsive surface resulting in an entropic force between them. We develop a method to calculate the entropic force, and detailed pressure distribution, for…
Recently, long and slender living worms have garnered significant interest because of their impressive ability to exhibit diverse emergent behaviors in highly entangled physical and topological conditions. These worms can form an active…
Nano-scale confinement of polymer in cone-shaped geometries occurs in many experimental situations. A flexible polymer confined in a cone-shaped nano-channel is studied theoretically and using molecular dynamics simulations. Distribution of…
The Langevin Equation for cooperative dynamics represents the dynamics of polymer melts with chains of increasing degree of polymerization, covering the full range of behavior from the unentangled to the entangled regime. This equation…
Polymer fibers consist of macromolecules oriented along the fiber axis. Better alignment of chains leads to an increased strength of the fiber. It is believed that the key factor preventing formation of a perfectly oriented fiber is…
We calculate the entanglement entropy of strongly correlated low-dimensional fermions in metallic, superfluid and antiferromagnetic insulating phases. The entanglement entropy reflects the degrees of freedom available in each phase for…
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…
The molecular dynamics simulations were used to obtain the radius of gyration of real ring polymer chains with different topological structures consisting of 360 monomers. We focus on the entropic force which is exerted by a dilute solution…
The tube model is a central concept in polymer physics, and allows to reduce the complex many-filament problem of an entangled polymer solution to a single filament description. We investigate the probability distribution function of…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
The conformational statistics of ring polymers in melts or dense solutions is strongly affected by their quenched microscopic topological state. The effect is particularly strong for untangled (i.e. non-concatenated and unknotted) rings,…
Contours associated to many interesting low-temperature statistical mechanics models (2D Ising model, (2+1)D SOS interface model, etc) can be described as self-interacting and self-avoiding walks on $\mathbb Z^2$. When the model is defined…
Inverse design can be a useful strategy for discovering interactions that drive particles to spontaneously self-assemble into a desired structure. Here, we extend an inverse design methodology--relative entropy optimization--to determine…
Semi-flexible polymers in crowded environments exhibit complex dynamics that play a crucial role in various biological and material design processes. Based on the classic reptation theory, it is generally believed that semiflexible polymers…
The interplay between the topological and geometrical properties of a polymer ring can be clarified by establishing the entanglement trapped in any portion (arc) of the ring. The task requires to close the open arcs into a ring, and the…
Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long distance regulatory interactions. The mechanistic basis…
We present Monte Carlo computer simulations for melts of semiflexible randomly knotted and randomly concatenated ring polymers on the fcc lattice and in slit confinement. Through systematic variation of the slit width at fixed melt density,…
Packing under confinement could generate rich ordered structures through entropic effects, which is a fundamental problem in condensed matter, biophysics and material science. The influence of confinement to the anisotropic hard…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
At sufficiently low temperatures and high densities, repulsive spherical particles in two-dimensions (2d) form close-packed structures with six-fold symmetry. By contrast, when the interparticle interaction has an attractive anisotropic…