Related papers: Theoretical study of the competition between foldi…
Optimizing paths on networks is crucial for many applications, from subway traffic to Internet communication. As global path optimization that takes account of all path-choices simultaneously is computationally hard, most existing routing…
In this paper we investigate the dynamical behavior of an interface or polymer, in interaction with a distant attractive substrate. The interface is modeled by the graph of a nearest neighbor path with non-negative integer coordinates, and…
This article introduces a model for interacting vertex-reinforced random walks, each taking values on a complete sub-graph of a locally finite undirected graph. The transition probability for a walk to a given vertex depends on the…
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…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
We consider a simple cubic lattice self-avoiding walk model of 3-star polymers adsorbed at a surface and then desorbed by pulling with an externally applied force. We determine rigorously the free energy of the model in terms of properties…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
We study by computer simulation a recently introduced generalised model of self-interacting self-avoiding trails on the square lattice that distinguishes two topologically different types of self-interaction: namely crossings where the…
Lattice model of directed self avoiding walk is used to investigate adsorption properties of a semiflexible sequential copolymer chain on an impenetrable curved surface on a hexagonal lattice in two dimensions. Walks of the copolymer chains…
We investigate the translocation dynamics of a folded linear polymer which is pulled through a nanopore by an external force. To this end, we generalize the iso-flux tension propagation (IFTP) theory for end-pulled polymer translocation to…
We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces.…
In the last twenty years network science has proven its strength in modelling many real-world interacting systems as generic agents, the nodes, connected by pairwise edges. Yet, in many relevant cases, interactions are not pairwise but…
We consider a system of self-avoiding polygons interacting through a potential that penalizes or rewards the number of mutual touchings and we provide an exact computation of the critical curve separating a regime of long polygons from a…
Contours associated to many interesting low-temperature statistical mechanics models (2D Ising model, (2+1)D SOS interface model, etc) can be described as self-interacting and self-avoiding walks on $\mathbb Z^2$. When the model is defined…
The depletion interaction between two parallel repulsive walls confining a dilute solution of long and flexible polymer chains is studied by field-theoretic methods. Special attention is paid to self-avoidance between chain monomers…
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…
In this article an anisotropic interaction model avoiding collisions is proposed. Starting point is a general isotropic interacting particle system, as used for swarming or follower-leader dynamics. An anisotropy is induced by rotation of…
We introduce a two-dimensional lattice model for the description of knotted polymer rings. A polymer configuration is modeled by a closed polygon drawn on the square diagonal lattice, with possible crossings describing pairs of strands of…
Advanced chain-growth computer simulation methodologies have been employed for a systematic statistical analysis of the critical behavior of a polymer adsorbing at a substrate. We use finitesize scaling techniques to investigate the…
We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced…