Related papers: Monte Carlo Results for Projected Self-Avoiding Po…
Monte Carlo simulations, using the PERM algorithm, of interacting self-avoiding walks (ISAW) and interacting self-avoiding trails (ISAT) in five dimensions are presented which locate the collapse phase transition in those models. It is…
We study a number of combinatorial and algebraic structures arising from walks on the two-dimensional integer lattice. To a given step set $X\subseteq\mathbb Z^2$, there are two naturally associated monoids: $\mathscr F_X$, the monoid of…
We examine the structure and dimensionality of the Jones polynomial using manifold learning techniques. Our data set consists of more than 10 million knots up to 17 crossings and two other special families up to 2001 crossings. We introduce…
In part I (math.PR/0406392) we proved for an arbitrary one-dimensional random walk with independent increments that the probability of crossing a level at a given time n is of the maximal order square root of n. In higher dimensions we call…
We computationally investigate the active transport of tangentially-driven polymers with varying degrees of flexibility and activity in two-dimensional square lattices of obstacles. Tight periodic confinement induces notable conformational…
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…
We consider $(1+1)$-dimensional directed polymers in a random potential and provide sufficient conditions guaranteeing joint localization. Joint localization means that for typical realizations of the environment, and for polymers started…
The conformations of interacting linear polymers on a dynamical planar random lattice are studied using a random two-matrix model. An exact expression for the partition function of self-avoiding chains subject to attractive contact…
Simulated configurations of flexible knotted rings confined inside a spherical cavity are fed into long-short term memory neural networks (LSTM NNs) designed to distinguish knot types. The results show that they perform well in knot…
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…
Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here we surprisingly observed that knotting can be very effectively produced in active polymers.…
Some recent work pointed out the usefulness of taking a large-deviation perspective when trying to extract anything resembling a macroscopic order parameter from a computer simulation. In this paper we note that the end-to-end distance of…
The conformational and electronic properties of conducting flexible random and self-avoiding walk polymer chains are under investigation. A Hamiltonian for conjugated flexible polymers is introduced and its physical consequences are…
We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation…
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…
Spontaneous formation of knots in long polymers at equilibrium is inevitable but becomes rare in sufficiently short chains. Here, we show that knotting and knot complexity increase by orders of magnitude in diblock polymers with a fraction…
A two-dimensional square-lattice model for the formation of secondary structures in proteins, the hydrogen-bonding model, is extended to include the effects of solvent quality. This is achieved by allowing configuration-dependent…
The investigation of freezing transitions of single polymers is computationally demanding, since surface effects dominate the nucleation process. In recent studies we have systematically shown that the freezing properties of flexible,…
We calculate improved lower bounds for the connective constants for self-avoiding walks on the square, hexagonal, triangular, $(4.8^2)$, and $(3.12^2)$ lattices. The bound is found by Kesten's method of irreducible bridges. This involves…
Polymers in a melt may be subject to topological constraints, as in the example of unlinked polymer rings. How to do statistical mechanics in the presence of such constraints remains a fundamental open problem. We study the effect of…