Related papers: CSAW: a dynamical model of protein folding
We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as…
In this paper, we introduce an approach to the protein folding problem from the point of view of statistical physics. Protein folding is a stochastic process by which a polypeptide folds into its characteristic and functional 3D structure…
We study the folding dynamics of polyalanine (Ala$_{20}$), a protein fragment with 20 residues whose native state is a single alpha helix. We use the CSAW model (conditioned self-avoiding walk), which treats the protein molecule as a chain…
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…
Self-avoiding walks (SAW) are the source of very difficult problems in probabilities and enumerative combinatorics. They are also of great interest as they are, for instance, the basis of protein structure prediction in bioinformatics.…
Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are…
Weakly self-avoiding walk (WSAW) is a model of simple random walk paths that penalizes self-intersections. On $\mathbb{Z}$, Greven and den Hollander proved in 1993 that the discrete-time weakly self-avoiding walk has an asymptotically…
If the three dimensional self-avoiding walk (SAW) is conformally invariant, then one can compute the hitting densities for the SAW in a half-space and in a sphere. The ensembles of SAW's used to define these hitting densities involve walks…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
The problems considered in the present paper have their roots in two different cultures. The 'true' (or myopic) self-avoiding walk model (TSAW) was introduced in the physics literature by Amit, Parisi and Peliti. This is a nearest neighbor…
Temporal networks serve as abstractions of many real-world dynamic systems. These networks typically evolve according to certain laws, such as the law of triadic closure, which is universal in social networks. Inductive representation…
Self-avoiding walks (SAWs) were introduced in chemistry to model the real-life behavior of chain-like entities such as solvents and polymers, whose physical volume prohibits multiple occupation of the same spatial point. In mathematics, a…
A planar self-avoiding walk (SAW) is a nearest neighbor random walk path in the square lattice with no self-intersection. A planar self-avoiding polygon (SAP) is a loop with no self-intersection. In this paper we present conjectures for the…
The myopic (or `true') self-avoiding walk model (MSAW) was introduced in the physics literature by Amit, Parisi and Peliti (1983). It is a random motion in Z^d pushed towards domains less visited in the past by a kind of negative gradient…
A growing self-avoiding walk (GSAW) is a stochastic process that starts from the origin on a lattice and grows by occupying an unoccupied adjacent lattice site at random. A sufficiently long GSAW will reach a state in which all adjacent…
We study various self-avoiding walks (SAWs) which are constrained to lie in the upper half-plane and are subjected to a compressive force. This force is applied to the vertex or vertices of the walk located at the maximum distance above the…
Recent findings suggest that processes such as the electronic energy transfer through the photosynthetic antenna display quantal features, aspects known from the dynamics of charge carriers along polymer backbones. Hence, in modeling energy…
We study via Monte Carlo simulation a generalisation of the so-called vertex interacting self-avoiding walk (VISAW) model on the square lattice. The configurations are actually not self-avoiding walks but rather restricted self-avoiding…
Various types of walks on complex networks have been used in recent years to model search and navigation in several kinds of systems, with particular emphasis on random walks. This gives valuable information on network properties, but…
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…