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By means of sophisticated Monte Carlo methods, we investigate the conformational phase diagram of a simple model for flexible polymers with explicit thickness. The thickness constraint, which is introduced geometrically via the global…
We present a detailed study of the structure-dynamics relationship of regio-regular and regio-random PEHT using different neutron scattering techniques. Deuteration is employed to modulate the coherent and incoherent cross-sections,…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
An active system consisting of many self-spinning dimers is simulated, and a distinct local rotational jamming transition is observed as the density increases. In the low density regime, the system stays in an absorbing state, in which each…
We analyze conformational properties of branched polymer structures, formed on the base of Erd\"os-R\'enyi random graph model. We consider networks with $N=5$ vertices and variable parameter $c$, that controls graph connectedness. The…
We investigate the dynamical behavior of rings around bodies whose shapes depart considerably from that of a sphere. To this end, we have developed a new self-gravitating discrete element N-body code, and employed a local simulation method…
Characteristics of relaxed density profile and conformation of polymer chains are studied by a Monte Carlo simulation on a discrete lattice in three dimensions using different segmental (kink-jump $K$, crank-shaft $C$, reptation $R$)…
In this paper we address the characterization of the structure of condensed materials, periodic and non-periodic. Carrying out an extensive study of over 7000 different groundstate structures of a 2D lattice model of binary packing, we find…
In the paper we investigate statistical and topological properties of fractional Brownian polymer chains, equipped with the short-range volume interactions. The attention is paid to statistical properties of collapsed conformations with the…
In this paper we examine the relative knotting probabilities in a lattice model of ring polymers confined in a cavity. The model is of a lattice knot of size $n$ in the cubic lattice, confined to a cube of side-length $L$ and with volume…
Topological constraints can affect both equilibrium and dynamic properties of polymer systems, and can play a role in the organization of chromosomes. Despite many theoretical studies, the effects of topological constraints on the…
We examine entanglements using monomer contacts between pairs of chains in a Brownian-dynamics simulation of a polymer melt. A map of contact positions with respect to the contacting monomer numbers (i,j) shows clustering in small regions…
We study surface effects in amorphous polymer systems by means of computer simulation. In the framework of molecular dynamics, we present two different methods to prepare such surfaces. {\em Free} surfaces are stabilized solely by…
Suppose we have an embedding of a graph $\mathbf{G}$ created by subdividing the edges of a simpler graph $\mathbf{G'}$. The edges of $\mathbf{G}$ can be divided into subsets which join pairs of ``junction'' vertices in $\mathbf{G'}$. The…
We investigate morphologies of semiflexible polymer rings, such as circular DNA, which are adsorbed onto topographically or chemically structured substrate surfaces. We classify all equilibrium morphologies for two striped surface…
The conformational properties of flexible and semiflexible polymers exposed to active noise are studied theoretically. The noise may originate from the interaction of the polymer with surround- ing active (Brownian) particles or from the…
Ring, or cyclic, polymers have unique properties compared to linear polymers, due to their topologically closed structure that has no beginning or end. Experimental measurements on molecular ring polymers are challenging due to their…
We define discrete constant mean curvature (cmc) surfaces in the three-dimensional Euclidean and Lorentz spaces in terms of sphere packings with orthogonally intersecting circles. These discrete cmc surfaces can be constructed from…
Topologically constrained genome-like polymers often double-fold into tree-like configurations. Here we calculate the exact number of tightly double-folded configurations available to a ring polymer in ideal conditions. For this purpose, we…
We prove some "high probability" results on the expected value of the mean width for random perturbations of random polytopes. The random perturbations are considered for Gaussian and $p$-stable random vectors, as well as uniform…