Related papers: Knots in Charged Polymers
Topological constraints (TCs) between polymers determine the behaviour of complex fluids such as creams, oils and plastics. Most of the polymer solutions used every day life employ linear chains; their behaviour is accurately captured by…
We present a computer simulation study of the compact self-avoiding loops as regards their length and topological state. We use a Hamiltonian closed path on the cubic-shaped segment of a 3D cubic lattice as a model of a compact polymer. The…
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
The most tight conformations of prime knots are found with the use of the SONO algorithm. Their curvature and torsion profiles are calculated. Symmetry of the knots is analysed. Connections with the physics of polymers are discussed.
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
Knots are entangled structures that cannot be untangled without a cut. Topological stability of knots is one of the many examples of their important properties that can be used in information storage and transfer. Knot dynamics is important…
We analyzed the localized charge dynamics in the system of $N$ interacting single-level quantum dots (QDs) coupled to the continuous spectrum states in the presence of Coulomb interaction between electrons within the dots. Different dots…
Scaling arguments are used to analyze the size of topologically constrained closed ring polymer with excluded volume. It is found that there exists a finite range of polymer thickness (excluded volume) in which self-avoidance is unimportant…
We investigate with numerical simulations the influence of topology and stiffness on macroscopic rheological properties of polymer melts consisting of unknotted, knotted or concatenated rings. While melts of flexible, knotted oligomer rings…
We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius…
A coarse-grained computational model is used to investigate how the bending rigidity of a polymer under tension affects the formation of a trefoil knot. Thermodynamic integration techniques are applied to demonstrate that the free-energy…
In this paper, we employ Molecular Dynamics computer simulations to study and compare the statics and dynamics of linear and circular (ring) polymer chains in entangled solutions of different densities. While we confirm that linear chain…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…
Hydrodynamic interactions as modeled by Multi-Particle Collision Dynamics can dramatically influence the dynamics of fully flexible, ring-shaped polymers in ways not known for any other polymer architecture or topology. We show that steady…
The statistical mechanics of single polymer knots is studied using Monte Carlo simulations. The polymers are considered on a cubic lattice and their conformations are randomly changed with the help of pivot transformations. After each…
A ring polymer in a confining space may exhibit at least two phases, namely an expanded (or solvent-rich phase) if its concentration is small, or a collapsed (or polymer-rich phase) when it is concentrated and compressed. These phases are…
Knot theory provides a powerful tool for the understanding of topological matters in biology, chemistry, and physics. Here knot theory is introduced to describe topological phases in the quantum spin system. Exactly solvable models with…
We present a methodology to simulate the mechanics of knots in elastic rods using geometrically nonlinear, full three-dimensional (3D) finite element analysis. We focus on the mechanical behavior of knots in tight configurations, for which…
The role of the topology and its relation with the geometry of biopolymers under different physical conditions is a nontrivial and interesting problem. Aiming at understanding this issue for a related simpler system, we use Monte Carlo…