Related papers: Computational investigations of folded self-avoidi…
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.…
The pivot algorithm for self-avoiding walks has been implemented in a manner which is dramatically faster than previous implementations, enabling extremely long walks to be efficiently simulated. We explicitly describe the data structures…
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…
We study self-avoiding walks on three-dimensional critical percolation clusters using a new exact enumeration method. It overcomes the exponential increase in computation time by exploiting the clusters' fractal nature. We enumerate walks…
Quantum walks exhibit many unique characteristics compared to classical random walks. In the classical setting, self-avoiding random walks have been studied as a variation on the usual classical random walk. Classical self-avoiding random…
A prototypical problem on which techniques for exact enumeration are tested and compared is the enumeration of self-avoiding walks. Here, we show an advance in the methodology of enumeration, making the process thousands or millions of…
We examine self-avoiding walks in dimensions 4 to 8 using high-precision Monte-Carlo simulations up to length N=16384, providing the first such results in dimensions $d > 4$ on which we concentrate our analysis. We analyse the scaling…
We reduce the problem of counting self-avoiding walks in the square lattice to a problem of counting the number of integral points in multidimensional domains. We obtain an asymptotic estimate of the number of self-avoiding walks of length…
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 study self-avoiding walks on the four-dimensional hypercubic lattice via Monte Carlo simulations of walks with up to one billion steps. We study the expected logarithmic corrections to scaling, and find convincing evidence in support the…
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 use new algorithms, based on the finite lattice method of series expansion, to extend the enumeration of self-avoiding walks and polygons on the triangular lattice to length 40 and 60, respectively. For self-avoiding walks to length 40…
We study the high-dimensional uniform prudent self-avoiding walk, which assigns equal probability to all nearest-neighbor self-avoiding paths of a fixed length that respect the prudent condition, namely, the path cannot take any step in the…
We study the correction-to-scaling exponents for the two-dimensional self-avoiding walk, using a combination of series-extrapolation and Monte Carlo methods. We enumerate all self-avoiding walks up to 59 steps on the square lattice, and up…
We introduce a fast implementation of the pivot algorithm for self-avoiding walks, which we use to obtain large samples of walks on the cubic lattice of up to $33 \times 10^6$ steps. Consequently the critical exponent $\nu$ for…
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…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
In two dimensions polymer collapse has been shown to be complex with multiple low temperature states and multi-critical points. Recently, strong numerical evidence has been provided for a long-standing prediction of universal scaling of…
In this paper we show the existence of three dimensional rigid, and thus unfoldable, lattice conformations. The structure we found has 450+ bonds, and we provide a computer assisted proof of the existence of such structures. The existence…
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…