相关论文: Writhe induced phase transition in unknotted self-…
When double stranded DNA is turned in experiments it undergoes a transition. We use an interacting self-avoiding walk on a three-dimensional fcc lattice weighted by writhe to relate to these experiments and treat this problem via…
We consider a simple lattice model of a topological phase transition in open polymers. To be precise, we study a model of self-avoiding walks on the simple cubic lattice tethered to a surface and weighted by an appropriately defined writhe.…
Phase transitions are ubiquitous phenomena, exemplified by the melting of ice and spontaneous magnetization of magnetic material. In general, a phase transition is associated with a symmetry breaking of a system; occurs due to the…
A simple solid-on-solid model of adsorbate-induced faceting is studied by using a modified Wang-Landau method. The phase diagram for this system is constructed by computing the density of states in a special two-dimensional energy space. A…
Motivated by experiments in which single DNA molecules are stretched and twisted we consider a perturbative approach around very high forces, where we determine the writhe distribution in a simple, analytically tractable model. Our results…
In this work, we combine coarse-grained Brownian dynamics simulations and mean-field theory to study supercoiling dynamics, as well as the steady-state profiles of twist and writhe, in an open DNA polymer where one of the free ends is…
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…
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…
We analyze a random lozenge tiling model of a large regular hexagon, whose underlying weight structure is periodic of period $2$ in both the horizontal and vertical directions. This is a determinantal point process whose correlation kernel…
We consider the phase transition induced by compressing a self-avoiding walk in a slab where the walk is attached to both walls of the slab in two and three dimensions, and the resulting phase once the polymer is compressed. The process of…
We consider a directed variant of the negative-weight percolation model in a two-dimensional, periodic, square lattice. The problem exhibits edge weights which are taken from a distribution that allows for both positive and negative values.…
Twisted two-dimensional (2D) layered materials exhibit many novel and unique phenomena, such as insulation and superconductivity transition, and superlubricity. However, the effect of twisting on these phenomena remains unclear. A key…
We study the pinning transition in a (1+1)-dimensional lattice model of a fluctuating interface interacting with a corrugated impenetrable wall. The interface is modeled as an $N$-step directed one-dimensional random walk on the half-line…
One-dimensional thermodynamic instabilities are phase transitions not prohibited by Landau's argument, because the energy of the domain wall (DW) which separates the two phases is infinite. Whether they actually occur in a given system of…
We study geometrical clues of a rigidity transition due to the emergence of a system-spanning state of self stress in under-constrained systems of individual polygons and spring networks constructed from such polygons. When a polygon with…
The phase structure of self-avoiding polymerized membranes is studied by extensive Hybrid Monte Carlo simulations. Several folding transitions from the flat to a collapsed state are found. Using a suitable order parameter and finite size…
The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
The unbinding properties of an interface near structured wedges are investigated by discrete models with short range interactions. The calculations demonstrate that interface unbinding take place in two stages: $i$) a continuous…
We apply a recently proposed criterion for the existence of phase transitions, which is based on the properties of the saddles of the energy landscape, to a simplified model of a system with gravitational interactions, referred to as the…