Related papers: Generalized-Ensemble Algorithms for the Isobaric-I…
Recently, industrial robots plays a significant role in intelligent manufacturing. Hence, it is an urgent issue to ensure the robot with the high positioning precision. To address this hot issue, a novel calibration method based on an…
The finite element method is a well-established method for the numerical solution of partial differential equations (PDEs), both linear and nonlinear. However, the repeated reassemblage of finite element matrices for nonlinear PDEs is…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
We present a physical formulation, and a numerical algorithm, based on a class of general order parameters for simulating the motion of a mixture of $N$ ($N\geqslant 2$) immiscible incompressible fluids with given densities, dynamic…
Recently, deep learning has emerged as a promising tool for statistical downscaling, the set of methods for generating high-resolution climate fields from coarse low-resolution variables. Nevertheless, their ability to generalize to climate…
We explored the composition dependence of a rather comprehensive set of properties of liquid water-ethanol mixtures by using the isobaric-isothermal molecular dynamics computer simulations. The united atom non-polarizable model from the…
The unitary dynamics of isolated quantum systems does not allow a pure state to thermalize. Because of that, if an isolated quantum system equilibrates, it will do so to the predictions of the so-called "diagonal ensemble" $\rho_{DE}$.…
Bayesian inference for factorial hidden Markov models is challenging due to the exponentially sized latent variable space. Standard Monte Carlo samplers can have difficulties effectively exploring the posterior landscape and are often…
In this work we investigate the theory for three different uni-directional population transfer schemes in trapped multilevel systems which can be utilized to cool molecular ions. The approach we use exploits the laser-induced coupling…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…
In this work a replica exchange Monte Carlo scheme which considers an extended isobaric-isothermal ensemble with respect to pressure is applied to study hard spheres (HS). The idea behind the proposal is expanding volume instead of…
We present several numerical results on granular mixtures. In particular, we examine the efficiency of diffusion as a mixing mechanism in these systems. The collisions are inelastic and to compensate the energy loss, we thermalize the…
Recently, Dammak and coworkers (H. Dammak, Y. Chalopin, M. Laroche, M. Hayoun, and J.J. Greffet. Quantumthermal bath for molecular dynamics simulation. Phys. Rev. Lett., 103:190601, 2009.) proposed that the quantum statistics of vibrations…
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…
We propose a novel Skew Gradient Embedding (SGE) framework for systematically reformulating thermodynamically consistent partial differential equation (PDE) models-capturing both reversible and irreversible processes-as generalized gradient…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
We improve a recently proposed dynamically driven renormalization group algorithm for cellular automata systems with one absorbing state, introducing spatial correlations in the expression for the transition probabilities. We implement the…
A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward…
In this paper, we analyze the embedding cell method, an algorithm which has been developed for the numerical homogenization of metal-ceramic composite materials. We show the convergence of the iteration scheme of this algorithm and the…
Integrable quantum many-body systems are considered to equilibrate to generalized Gibbs ensembles (GGEs) characterized by the expectation values of integrals of motion. We study the dynamics of exactly solvable quadratic bosonic systems in…