Related papers: Efficient Monte Carlo algorithm and high-precision…
A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…
Using Monte Carlo simulations on different system sizes we determine with high precision the critical thresholds of two families of directed percolation models on a square lattice. The thresholds decrease exponentially with the degree of…
The asymptotic behavior of the percolation threshold $p_c$ and its dependence upon coordination number $z$ is investigated for both site and bond percolation on four-dimensional lattices with compact extended neighborhoods. Simple…
This article presents an algorithm that generates a conservative confidence interval of a specified length and coverage probability for the power of a Monte Carlo test (such as a bootstrap or permutation test). It is the first method that…
We recently demonstrated that standard fixed-time lattice random-walk models cannot be modified to properly represent biased diffusion processes in more than two dimensions. The origin of this fundamental limitation appears to be the fact…
A lattice-based model for continuum percolation is applied to the case of randomly located, partially aligned sticks with unequal lengths in 2D which are allowed to cross each other. Results are obtained for the critical number of sticks…
We propose an efficient method for Monte Carlo simulation of quantum lattice models. Unlike most other quantum Monte Carlo methods, a single run of the proposed method yields the free energy and the entropy with high precision for the whole…
This article presents a Monte Carlo study on bond percolation in distorted square and triangular lattices. The distorted lattices are generated by dislocating the sites from their regular positions. The amount and direction of the…
Bootstrap percolation on a graph is a deterministic process that iteratively enlarges a set of occupied sites by adjoining points with at least $\theta$ occupied neighbors. The initially occupied set is random, given by a uniform product…
We introduce a Monte-Carlo algorithm for the simulation of charged particles moving in the continuum. Electrostatic interactions are not instantaneous as in conventional approaches, but are mediated by a constrained, diffusing electric…
Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
We investigate bond- and site-percolation models on several two-dimensional lattices numerically, by means of transfer-matrix calculations and Monte Carlo simulations. The lattices include the square, triangular, honeycomb kagome and diced…
Among random sampling methods, Markov Chain Monte Carlo algorithms are foremost. Using a combination of analytical and numerical approaches, we study their convergence properties towards the steady state, within a random walk Metropolis…
Obtaining reliable estimates of the statistical properties of complex macromolecules by computer simulation is a task that requires high computational effort as well as the development of highly efficient simulation algorithms. We present…
We develop off-lattice simulations of semiflexible polymer chains subjected to applied mechanical forces using Markov Chain Monte Carlo. Our approach models the polymer as a chain of fixed-length bonds, with configurations updated through…
In this paper we study bond percolation on a one-dimensional chain with power-law bond probability $C/ r^{1+\sigma}$, where $r$ is the distance length between distinct sites. We introduce and test an order $N$ Monte Carlo algorithm and we…
In this paper we study statistical methods of parameters estimation of the site percolation model. Advantages of the proposed method is demonstrated for the computing of the confidence interval of mass fractal dimension of a percolation…
We investigate the process of invasion percolation between two sites (injection and extraction sites) separated by a distance r in two-dimensional lattices of size L. Our results for the non-trapping invasion percolation model indicate that…
We study uniform 3-star polymers with one branch tethered to an attractive surface and another branch pulled by a force away from the surface. Each branch of the 3-star lattice is modelled as a self-avoiding walk on the simple cubic lattice…