Related papers: Prediction of Peptide Conformation by the Multican…
Monte Carlo simulation with {\it a-priori} unknown weights have attracted recent attention and progress has been made in understanding (i) the technical feasibility of such simulations and (ii) classes of systems for which such simulations…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
We present a novel implementation of the parallel tempering Monte Carlo method in a multicanonical ensemble. Multicanonical weights are derived by a self-consistent iterative process using a Boltzmann inversion of global energy histograms.…
We describe a simple ansatz to approximate the low temperature behavior of proteins and peptides by a mean-field-like model which is analytically solvable. For a small peptide some thermodynamic quantities are calculated and compared with…
A simple Monte Carlo (MC) algorithm for the simulation of the passage of low-energy gamma rays and electrons through any material medium is presented. The algorithm includes several approximations that accelerate the simulation while…
In complex systems such as spin systems and protein systems, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the generalized-ensemble algorithms in order to overcome this…
We propose a description of pairing properties in finite systems within the canonical and microcanonical ensembles. The approach is derived by solving the BCS and self-consistent quasiparticle random-phase approximation with the…
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…
Calculating thermodynamic potentials and observables efficiently and accurately is key for the application of statistical mechanics simulations to materials science. However, naive Monte Carlo approaches, on which such calculations are…
This paper describes an isobaric semi-grand canonical ensemble Monte Carlo scheme for the accurate study of phase behaviour in ternary fluid mixtures under the experimentally relevant conditions of prescribed pressure, temperature and…
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…
Conventional simulations of complex systems in the canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble overcomes this difficulty by performing a random walk in potential energy space and other…
We present a method to facilitate Monte Carlo simulations in the grand canonical ensemble given a target mean particle number. The method imposes a fictitious dynamics on the chemical potential, to be run concurrently with the Monte Carlo…
A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo J. Chem.…
Several approximations are made to study the microcanonical formalism that are valid in the thermodynamics limit. Usually it is assumed that: 1)Stirling approximation can be used to evaluate the number of microstates; 2) the surface entropy…
A framework is presented for carrying out simulations of equilibrium systems in the microcanonical ensemble using annealing in an energy ceiling. The framework encompasses an equilibrium version of simulated annealing, population annealing…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
We study the thermodynamic properties of the three-dimensional Blume-Capel model on the simple cubic lattice by means of computer simulations. In particular, we implement a parallelized variant of the multicanonical approach and perform…
An efficient Path Integral Monte Carlo procedure is proposed to simulate the behavior of quantum many-body dissipative systems described within the framework of the influence functional. Thermodynamic observables are obtained by Monte Carlo…
The multiscale Monte-Carlo algorithm outlined in Bai and Brandt[1] is applied to a simple model of the polypeptide backbone. Effective coarse level Hamiltonians are derived by a fast Newtonian iterative scheme. The coarse Hamiltonian…