Related papers: Information Loss in Coarse Graining of Polymer Con…
We perform a Monte Carlo study of $N$-step self-avoiding walks, attached to the corner of an impenetrable wedge in two dimensions ($d=2$), or the tip of an impenetrable cone in $d=3$, of sizes ranging up to $N=10^6$ steps. We find that the…
Directed paths have been used extensively in the scientific literature as a model of a linear polymer. Such paths models in particular the conformational entropy of a linear polymer and the effects it has on the free energy. These directed…
Self-avoiding walk (SAW) represents linear polymer chain on a large scale, neglecting its chemical details and emphasizing the role of its conformational statistics. The role of the latter is important in formation of agglomerates and…
The self-avoid random walk algorithm has been extensively used in the study of polymers. In this work we study the basic properties of the trajectories generated with this algorithm when two interactions are added to it: contact and folding…
We study a generalized interacting self-avoiding walk (ISAW) model with nearest- and next nearest-neighbor (NN and NNN) interactions on the square and cubic lattices. In both dimensions, the phase diagrams show coil and globule phases…
A contact map is a simple representation of the structure of proteins and other chain-like macromolecules. This representation is quite amenable to numerical studies of folding. We show that the number of contact maps corresponding to the…
Oriented self-avoiding walks (OSAWs) on a square lattice are studied, with binding energies between steps that are oriented parallel across a face of the lattice. By means of exact enumeration and Monte Carlo simulation, we reconstruct the…
Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length $N \sim {\cal O}(10^4)$. Based on the standard simple…
In polymer physics it is typically assumed that excluded volume interactions are effectively screened in polymer melts. Hence, chains could be described by an effective random walk without excluded volume interactions. In this letter, we…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
Polymer chains with hard-core interaction on a two-dimensional lattice are modeled by directed random walks. Two models, one with intersecting walks (IW) and another with non-intersecting walks (NIW) are presented, solved and compared. The…
We argue that the mean crossing number of a random polymer configuration is simply a measure of opacity, without being closely related to entanglement as claimed by several authors. We present an easy way of estimating its asymptotic…
The exact grand-canonical solution of a generalized interacting self-avoid walk (ISAW) model, placed on a Husimi lattice built with squares, is presented. In this model, beyond the traditional interaction $\omega_1=e^{\epsilon_1/k_B T}$…
We study self-avoiding walks on the square lattice restricted to a square box of side $L$ weighted by a length fugacity without restriction of their end points. This models a confined polymer in dilute solution. The model admits a phase…
We prove tight mixing time bounds for natural random walks on bases of matroids, determinantal distributions, and more generally distributions associated with log-concave polynomials. For a matroid of rank $k$ on a ground set of $n$…
Single three dimensional polymers confined to a slab, i.e. to the region between two parallel plane walls, are studied by Monte Carlo simulations. They are described by $N$-step walks on a simple cubic lattice confined to the region $1 \le…
It is well known that the weak limit of a suitably scaled continuous-time random walk (CTRW) is the Brownian motion. We investigate the convergence of certain patterned random matrices whose entries are independent CTRWs and their…
We consider a simple random walk of length $N$, denoted by $(S_{i})_{i\in \{1,...,N\}}$, and we define $(w_i)_{i\geq 1}$ a sequence of centered i.i.d. random variables. For $K\in\N$ we define $((\gamma_i^{-K},...,\gamma_i^K))_{i\geq 1}$ an…
Based on transfer matrix techniques and finite size scaling, we study the oriented polymer (self-avoiding walk) with nearest neighbor interaction. In the repulsive regime, various critical exponents are computed and compared with exact…
In this paper we present a new and flexible method to show that, in one dimension, various self-repellent random walks converge to self-repellent Brownian motion in the limit of weak interaction after appropriate space-time scaling. Our…