Related papers: Metastable tight knots in a worm-like polymer
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…
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 present a unified theory for the longitudinal dynamic response of a stiff polymer in solution to various external perturbations (mechanical excitations, hydrodynamic flows, electrical fields, temperature quenches ...) that can be…
We obtain the entropy of flexible linear chains composed of M monomers placed on the square lattice using a transfer matrix approach. An excluded volume interaction is included by considering the chains to be self-and mutually avoiding, and…
This report presents a unified treatment of the density of states for the knots and folds of polymer chains. The physical realization of such systems ranges from DNA molecules to the microscopic configurations of space-time.
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 investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
We consider the probability of knotting in equilateral random polygons in Euclidean 3-dimensional space, which model, for instance, random polymers. Results from an extensive Monte Carlo dataset of random polygons indicate a universal…
We prove the fractal crumpled structure of collapsed unknotted polymer ring. In this state the polymer chain forms a system of densely packed folds, mutually separated in all scales. The proof is based on the numerical and analytical…
We consider a model for a polymer chain interacting with a sequence of equispaced flat interfaces through a pinning potential. The intensity $\delta \in \mathbb {R}$ of the pinning interaction is constant, while the interface spacing…
A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…
The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…
We present a model for semiflexible polymers in Hamiltonian formulation which interpolates between a Rouse chain and worm-like chain. Both models are realized as limits for the parameters. The model parameters can also be chosen to match…
Large scale molecular dynamics simulations on graphic processing units (GPUs) are employed to study the scaling behavior of ring polymers with various topological constraints in melts. Typical sizes of rings containing $3_1$, $5_1$ knots…
We study numerically the tightness of prime flat knots in a model of self-attracting polymers with excluded volume. We find that these knots are localised in the high temperature swollen regime, but become delocalised in the low temperature…
We study several related models of self-avoiding polygons in a tubular subgraph of the simple cubic lattice, with a particular interest in the asymptotics of the knotting statistics. Polygons in a tube can be characterised by a finite…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
We perform Transition matrix Monte Carlo simulations to evaluate the entropy of rhombus tilings with fixed polygonal boundaries and 2D-fold rotational symmetry. We estimate the large-size limit of this entropy for D=4 to 10. We confirm…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…