Related papers: Knots as Topological Order Parameter For Semi-Flex…
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…
Phase diagrams of charged semi-hard-core bosons are studied in the mean field approximation. An increase in the parameter of local correlations is shown to lead to the transformation of the phase diagram of the system from the form…
The nature of the globule-coil transition of surface-confined polymers has been an issue of debate. Here this 2D collapse transition is studied through a partially directed lattice model. In the general case of polymers with positive…
Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the…
We consider a stiff polymer chain in poor solvent and apply a force at one end of the chain. We find that by varying the stiffness parameter, polymer undergoes a transition from the globule state to the folded like state. The conformation…
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…
We demonstrate that a semiflexible bundle of wormlike chains exhibits a state-dependent bending stiffness that alters fundamentally its scaling behavior with respect to the standard wormlike chain. We explore the equilibrium conformational…
We study by Monte Carlo simulations a model of knotted polymer ring adsorbing onto an impenetrable, attractive wall. The polymer is described by a self-avoiding polygon (SAP) on the cubic lattice. We find that the adsorption transition…
We use computer simulations to compare the dynamical behaviour of torus and even-twist knots in polymers under tension. The knots diffuse through a mechanism similar to reptation. Their friction coefficients grow linearly with average knot…
Using molecular dynamics simulations of a tangent-soft-sphere bead-spring polymer model, we examine the degree to which semiflexible polymer melts solidify at isostaticity. Flexible and stiff chains crystallize when they are isostatic as…
Brownian motion and viscoelasticity of semiflexible polymers is a subject that has been studied for many years. Still, rigorous analysis has been hindered due to the difficulty in handling the constraint that polymer chains cannot be…
Many experiments have been done to determine the relative strength of different knots, and these show that the break in a knotted rope almost invariably occurs at a point just outside the `entrance' to the knot. The influence of knots on…
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…
We study the dynamics of a knot in a semiflexible polymer confined to a narrow channel of width comparable to the polymers' persistence length. Using a combination of Brownian dynamics simulations and a coarse-grained stochastic model, we…
We map out the solid-state morphologies formed by model soft-pearl-necklace polymers as a function of bending stiffness $k_b$ spanning the range from fully flexible to rodlike chains. The ratio of Kuhn length to bead diameter ($l_K/r_0$)…
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…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their…
We use numerical simulations to study tangentially active flexible ring polymers with different knot topologies. Simple, unknotted active rings display a transition from an extended phase to a collapsed one upon increasing the degree of…
We present a braided circuit topology framework for investigating topology and structural phase transitions in aggregates of semiflexible polymers. In the conventional approach to circuit topology, which specifically applies to single…