Related papers: Prediction of Peptide Conformation by the Multican…
In this work, we develop an atomistic, graph-based kinetic Monte Carlo (KMC) simulation routine to predict crystal morphology. Within this routine, we encode the state of the supercell in a binary occupation vector and the topology of the…
A new parallelized simulation code is presented, which uses a Monte Carlo method to determine particle spectra in the KATRIN source. Reaction chains are generated from the decay of tritium within the source. The code includes all relevant…
We have performed exhaustive multicanonical Monte Carlo simulations of three 12-residue synthetic peptides in order to investigate the thermodynamic and structural properties as well as the characteristic helix-coil transitions. In these…
We propose a new recursive procedure to estimate the microcanonical density of states in multicanonical Monte Carlo simulations which relies only on measurements of moments of the energy distribution, avoiding entirely the need for energy…
In this manuscript, we describe a new configurational bias Monte Carlo technique for the simulation of peptides. We focus on the biologically relevant cases of linear and cyclic peptides. Our approach leads to an efficient,…
We investigate how the temperature calculated from the microcanonical entropy compares with the canonical temperature for finite isolated quantum systems. We concentrate on systems with sizes that make them accessible to numerical exact…
Predicting structural and energetic properties of a molecular system is one of the fundamental tasks in molecular simulations, and it has use cases in chemistry, biology, and medicine. In the past decade, the advent of machine learning…
The heat capacity and isomer distributions of the 38 atom Lennard-Jones cluster have been calculated in the canonical ensemble using parallel tempering Monte Carlo methods. A distinct region of temperature is identified that corresponds to…
It is a long-standing challenge to accurately and efficiently compute thermodynamic quantities of many-body systems at thermal equilibrium. The conventional methods, e.g., Markov chain Monte Carlo, require many steps to equilibrate. The…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
A Kallen-Lehman approach to 3D Ising model is analyzed numerically both at low and high temperature. It is shown that, even assuming a minimal duality breaking, one can fix three parameters of the model to get a very good agreement with the…
The sensitivity of the Statistical Multifragmentation Model to the underlying statistical assumptions is investigated. We concentrate on its micro-canonical, canonical, and isobaric formulations. As far as average values are concerned, our…
Using a one-parameter case as an example, we demonstrate that multicanonical simulations allow for accurate estimates of the residual combinatorial entropy of partially ordered ice. For the considered case corrections to an (approximate)…
We show that the acceptance probability for swaps in the parallel tempering Monte Carlo method for classical canonical systems is given by a universal function that depends on the average statistical fluctuations of the potential and on the…
Quantum mechanics for many-body systems may be reduced to the evaluation of integrals in 3N dimensions using Monte-Carlo, providing the Quantum Monte Carlo ab initio methods. Here we limit ourselves to expectation values for trial…
The results of numerical simulation using a modified Monte Carlo method with a heat bath algorithm for the pseudospin model of cuprates are presented. The temperature phase diagrams are constructed for various degrees of doping and for…
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…
A systematic comparison is conducted for pairing properties of finite systems at nonzero temperature as predicted by the exact solutions of the pairing problem embedded in three principal statistical ensembles, as well as the unprojected…
An extensive Quantum Monte Carlo calculation is performed for the two-leg Hubbard ladder model to clarify whether the singlet pairing correlation decays slowly, which is predicted from the weak-coupling theory but controversial from…
It has been proved for a class of mean-field and long-range systems that the concavity of the thermodynamic entropy determines whether the microcanonical and canonical ensembles are equivalent at the level of their equilibrium states, i.e.,…