Related papers: Protein structure prediction software generate two…
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…
To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D…
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…
This is a rather personal review of the problem of self-avoiding walks and polygons. After defining the problem, and outlining what is known rigorously and what is merely conjectured, I highlight the major outstanding problems. I then give…
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…
A celebrated problem in numerical analysis is to consider Brownian motion originating at the centre of a $10 \times 1$ rectangle, and to evaluate the ratio of probabilities of a Brownian path hitting the short ends of the rectangle before…
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…
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…
Let D be a domain in the plane containing the origin. We are interested in the ensemble of self-avoiding walks (SAW's) in D which start at the origin and end on the boundary of the domain. We introduce an ensemble of SAW's that we expect to…
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…
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…
Simulations of the self-avoiding walk (SAW) are performed in a half-plane and a cut-plane (the complex plane with the positive real axis removed) using the pivot algorithm. We test the conjecture of Lawler, Schramm and Werner that the…
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…
In recent years, advances in artificial intelligence (AI) have transformed structural biology, particularly protein structure prediction. Though AI-based methods, such as AlphaFold (AF), often predict single conformations of proteins with…
Several kinds of walks on complex networks are currently used to analyze search and navigation in different systems. Many analytical and computational results are known for random walks on such networks. Self-avoiding walks (SAWs) are…
We study the connective constants of weighted self-avoiding walks (SAWs) on infinite graphs and groups. The main focus is upon weighted SAWs on finitely generated, virtually indicable groups. Such groups possess so-called 'height…
CSAW (conditioned self-avoiding walk) is a model of protein folding that combines SAW (self-avoiding walk) with Monte-Carlo. It simulates the Brownian motion of a chain molecule in the presence of interactions, both among chain residues,…
This article presents SAWdoubler, a package for counting the total number Z(N) of self-avoiding walks (SAWs) on a regular lattice by the length-doubling method, of which the basic concept has been published previously by us. We discuss an…
A comprehensive numerical study of self-avoiding walks (SAW's) on randomly diluted lattices in two and three dimensions is carried out. The critical exponents $\nu$ and $\chi$ are calculated for various different occupation probabilities,…
This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence.…