相关论文: Grand-Canonical Adaptive Resolution Centroid Molec…
We introduce a new micro-macro Markov chain Monte Carlo method (mM-MCMC) to sample invariant distributions of molecular dynamics systems that exhibit a time-scale separation between the microscopic (fast) dynamics, and the macroscopic…
This paper introduces a new method for minimizing matrix-smooth non-convex objectives through the use of novel Compressed Gradient Descent (CGD) algorithms enhanced with a matrix-valued stepsize. The proposed algorithms are theoretically…
Computational magnetohydrodynamics (MHD) for space physics has become an essential area in understanding the multiscale dynamics of geophysical and astrophysical plasma processes, partially motivated by the lack of space data. Full MHD…
Dimensionality reduction represents a crucial step in extracting meaningful insights from Molecular Dynamics (MD) simulations. Conventional approaches, including linear methods such as principal component analysis as well as various…
To accurately study chemical reactions in the condensed phase or within enzymes, both a quantum-mechanical description and sufficient configurational sampling is required to reach converged estimates. Here, quantum mechanics/molecular…
We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of…
When numerically solving partial differential equations, for a given problem and operating condition, adaptive mesh refinement (AMR) has proven its efficiency to automatically build a discretization achieving a prescribed accuracy at low…
We investigate multi-component metallic glass systems using a hybrid Molecular Dynamics (MD) and Variance-Constrained Semi-Grand Canonical approach. This method enables us to generate samples with properties consistent with experimental…
Conventional molecular dynamics (MD) simulation approaches, such as $\textit{ab initio}$ MD (AIMD) and empirical force field MD (EFFMD), face significant trade-offs between physical accuracy and computational efficiency. This work presents…
In this paper, we develop a computational multiscale to solve the parabolic wave approximation with heterogeneous and variable media. Parabolic wave approximation is a technique to approximate the full wave equation. One benefit of the…
We discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within…
The emergence of new nanoporous materials, based e.g. on 2D materials, offers new avenues for water filtration and energy. There is accordingly a need to investigate the molecular mechanisms at the root of the advanced performances of these…
This paper develops novel and robust central discontinuous Galerkin (CDG) schemes of arbitrarily high-order accuracy for special relativistic magnetohydrodynamics (RMHD) with a general equation of state (EOS). These schemes are provably…
Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles…
A second-order face-centred finite volume strategy on general meshes is proposed. The method uses a mixed formulation in which a constant approximation of the unknown is computed on the faces of the mesh. Such information is then used to…
In this paper, we study a sequential decision-making problem, called Adaptive Sampling for Discovery (ASD). Starting with a large unlabeled dataset, algorithms for ASD adaptively label the points with the goal to maximize the sum of…
Hyper-parameter optimization remains as the core issue of Gaussian process (GP) for machine learning nowadays. The benchmark method using maximum likelihood (ML) estimation and gradient descent (GD) is impractical for processing big data…
We describe a new algorithm for simulating complex Markoff-processes. We have used a reaction-cell method in order to simulate arbitrary reactions. It can be used for any kind of RDS on arbitrary topologies, including fractal dimensions or…
Microscopic processes on surfaces such as adsorption, desorption, diffusion and reaction of interacting particles can be simulated using kinetic Monte Carlo (kMC) algorithms. Even though kMC methods are accurate, they are computationally…
Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper,…