Related papers: Protein folding simulations with Interacting Growt…

We propose an algorithm based on local growth rules for kinetically generating self avoiding walk configurations at any given temperature. This algorithm, called the Interacting Growth Walk (IGW) algorithm, does not suffer from attrition on…

We show that the compact self avoiding walk configurations, kinetically generated by the recently introduced Interacting Growth Walk (IGW) model, can be considered as members of a canonical ensemble if they are assigned random values of…

Interacting Growth Walks is a recently proposed stochastic model for studying the coil-globule transition of linear polymers. We propose a flat energy histogram version for Interacting Growth Walk. We demonstrate the algorithm on two…

The Interacting Growth Walk (IGW) is a kinetic algorithm proposed recently for generating long, compact, self avoiding walks. The growth process in IGW is tuned by the so called growth temperature $T' = 1/(k_B \beta ')$. On a square lattice…

We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and…

We describe a class of growth algorithms for finding low energy states of heteropolymers. These polymers form toy models for proteins, and the hope is that similar methods will ultimately be useful for finding native states of real proteins…

We show that the Density of States (DoS) for lattice Self Avoiding Walks can be estimated by using an inverse algorithm, called flatIGW, whose step-growth rules are dynamically adjusted by requiring the energy histogram to be locally flat.…

The HP model of protein folding, where the chain exists in a free medium, is investigated using a parallel Monte Carlo scheme based upon Wang-Landau sampling. Expanding on the work of Wust and Landau by introducing a lesser known replica…

We have explained in detail why the canonical partition function of Interacting Self Avoiding Walk (ISAW), is exactly equivalent to the configurational average of the weights associated with growth walks, such as the Interacting Growth Walk…

We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular…

Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…

Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very…

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…

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 protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…

Self-avoiding walks are studied on the 3-simplex fractal lattice as a model of linear polymer conformations in a dilute, non-homogeneous solution. A model is supplemented with bending energies and attractive-interaction energies between…

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…

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…

This paper is dedicated to the investigation of a $1+1$ dimensional self-interacting and partially directed self-avoiding walk, usually referred to by the acronym IPDSAW and introduced in \cite{ZL68} by Zwanzig and Lauritzen to study the…

We study a generalized interacting self-avoiding walk (ISAW) model with nearest- and next nearest-neighbor (NN and NNN) interactions on the square and cubic lattices. In both dimensions, the phase diagrams show coil and globule phases…