Related papers: Multicanonical Chain Growth Algorithm
The basic problem in equilibrium statistical mechanics is to compute phase space average, in which Monte Carlo method plays a very important role. We begin with a review of nonlocal algorithms for Markov chain Monte Carlo simulation in…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
We characterize the equation of state for a simple three-dimensional DNA hairpin model using a Metropolis Monte Carlo algorithm. This algorithm was run at constant temperature and fixed separation between the terminal ends of the strand.…
There is significant interest in rapid protein simulations because of the time-scale limitations of all-atom methods. Exploiting the low cost and great availability of computer memory, we report a Monte Carlo technique for incorporating…
We describe an efficient Monte Carlo algorithm using a random walk in energy space to obtain a very accurate estimate of the density of states for classical statistical models. The density of states is modified at each step when the energy…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P. Grassberger, Phys. Rev. E, in press (1997)) leads to extremely efficient algorithms for the folding of simple model proteins. We test it on several models…
The diffusion Monte Carlo method with symmetry-based state selection is used to calculate the quantum energy states of H$_2^+$ confined into potential barriers of atomic dimensions (a model for these ions in solids). Special solutions are…
We present a new and general Monte Carlo iteration method for generalized ensembles. It consists of two elements: (1) a simple algorithm to distinguish between distributions arising from respectively equilibrium- and non-equilibrium…
Efficient and accurate algorithm for partition function, free energy and thermal entropy calculations is of great significance in statistical physics and quantum many-body physics. Here we present an unbiased but low-technical-barrier…
A Monte Carlo method based on a density-of-states sampling is proposed for study of arbitrary statistical mechanical ensembles in a continuum. A random walk in the two-dimensional space of particle number and energy is used to estimate the…
In any valid Monte Carlo sampling that realizes microcanonical property we can collect statistics for a transition matrix in energy. This matrix is used to determine the density of states, from which most of the thermodynamical averages can…
Monte Carlo simulations using Wang-Landau sampling are performed to study three-dimensional chains of homopolymers on a lattice. We confirm the accuracy of the method by calculating the thermodynamic properties of this system. Our results…
Histogram-reweighting Monte Carlo simulations were used to obtain polymer / solvent phase diagrams for lattice homopolymers of chain lengths up to r=1000 monomers. The simulation technique was based on performing a series of grand canonical…
Microcanonical thermostatistics analysis has become an important tool to reveal essential aspects of phase transitions in complex systems. An efficient way to estimate the microcanonical inverse temperature $\beta(E)$ and the microcanonical…
We discuss electronic properties and their evolution for the linear chain of $H_2$ molecules in the presence of a uniform external force $f$ acting along the chain. The system is described by an extended Hubbard model within a fully…
We present density response estimators for Monte Carlo simulations that are based on a reweighting procedure, where the samples of an unperturbed system are used to estimate the properties of a system perturbed by an external harmonic…
Canonical ensembles consisting of $M$-unit $Hubbard$ $dimers$ have been studies within the nonextensive statistics (NES). The temperature dependences of the energy, entropy, specific heat and susceptibility have been calculated for the…
We present a method for the direct evaluation of the difference between the free energies of two crystalline structures, of different symmetry. The method rests on a Monte Carlo procedure which allows one to sample along a path, through…
We explore a self-learning Markov chain Monte Carlo method based on the Adversarial Non-linear Independent Components Estimation Monte Carlo, which utilizes generative models and artificial neural networks. We apply this method to the…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…