Related papers: Flat histogram simulation of lattice polymer syste…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
We point out that a newly introduced recursive algorithm for lattice polymers has a much wider range of applicability. In particular, we apply it to the simulation of off-lattice polymers with Lennard-Jones potentials between non-bonded…
Whether a system is to be considered complex or not depends on how one searches for correlations. We propose a general scheme for calculation of entropies in lattice systems that has high flexibility in how correlations are successively…
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…
A general method is presented for modeling high entropy alloys as ensembles of randomly sampled, ordered configurations on a given lattice. Statistical mechanics is applied post hoc to derive the ensemble properties as a function of…
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…
Flat histogram methods, such as Wang--Landau sampling, provide a means for high-throughput calculation of phase diagrams of atomistic/lattice model systems. Many parallelisation schemes with varying degrees of complexity have been proposed…
In the context of Monte Carlo sampling for lattice models, the complexity of the energy landscape often leads to Markov chains being trapped in local optima, thereby increasing the correlation between samples and reducing sampling…
Graphity models are characterized by configuration spaces in which states correspond to graphs and Hamiltonians that depend on local properties of graphs such as the degrees of vertices and numbers of short cycles. As statistical systems,…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
In this work we illustrate our novel quantitative simulation approach for dense amorphous polymer systems, as discussed in our previous work[Kulkarni et al., A Novel Approach for Lattice Simulations of Polymer Chains in Dense Amorphous…
Accelerated algorithms for simulating the morphological evolution of strained heteroeptiaxy based on a ball and spring lattice model in three dimensions are explained. We derive exact Green's function formalisms for boundary values in the…
Among lattice configurations of densely packed hard ellipses, Monte Carlo simulations are used to identify the so-called parallel and diagonal lattices as the two favourable states. The free energies of these two states are computed for…
In this paper we present simulations of a surface-adsorbed polymer subject to an elongation force. The polymer is modelled by a self-avoiding walk on a regular lattice. It is confined to a half-space by an adsorbing surface with attractions…
The Hamiltonian Monte Carlo method generates samples by introducing a mechanical system that explores the target density. For distributions on manifolds it is not always simple to perform the mechanics as a result of the lack of global…
We present a new way to compute thermodynamical observables on the lattice. We compute excited states and thermodynamical functions in the scalar model via the Monte Carlo Hamiltonian technique. We find agreement with standard Lagrangian…
We present a lattice Monte Carlo algorithm based on the one originally proposed by Maggs and Rossetto for simulating electrostatic interactions in inhomogeneous dielectric media. The original algorithm is known to produce attractive…
We propose a method for efficient simulations in extended ensembles, useful, e.g., for the study of problems with complex energy landscapes and for free energy calculations. The main difficulty in such simulations is the estimation of the a…
In order to perform numerical studies of long-term stability in nonlinear Hamiltonian systems, one needs a numerical integration algorithm which is symplectic. Further, this algorithm should be fast and accurate. In this paper, we propose…
A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are…