Related papers: The ENUF Method -- Ewald Summation based on Non-Un…
The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano-/micro- scale. The method shows great potential to solve the computational bottleneck of long-range…
Ensemble methods such as the Ensemble Kalman Filter (EnKF) are widely used for data assimilation in large-scale geophysical applications, as for example in numerical weather prediction (NWP). There is a growing interest for physical models…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
The efficient simulation of fluid-structure interactions at zero Reynolds number requires the use of fast summation techniques in order to rapidly compute the long-ranged hydrodynamic interactions between the structures. One approach for…
A lattice dynamical formalism based on nonaffine response theory is derived for non-centrosymmetric crystals, accounting for long-range interatomic interactions using the Ewald method. The framework takes equilibrated static configurations…
The Biot-Savart law is relevant in physical contexts including electromagnetism and fluid dynamics. In the latter case, when the rotation of a fluid is confined to a set of very thin vortex filaments, this law describes the velocity field…
Combustion stabilization and enhancement of the flammability limits are mandatory objectives to improve nowadays combustion chambers. At this purpose, the use of an electric field in the flame region provides a solution which is, at the…
We show how to evaluate mobility profiles, characterizing the transport of confined fluids under a perturbation, from equilibrium molecular simulations. The correlation functions derived with the Green-Kubo formalism are difficult to sample…
The accuracy of Earth system models is compromised by unknown and/or unresolved dynamics, making the quantification of systematic model errors essential. While a model parameter estimation, which allows parameters to change…
The smooth particle mesh Ewald (SPME) method is an FFT based method for the fast evaluation of electrostatic interactions under periodic boundary conditions. A highly optimized implementation of this method is available in GROMACS, a widely…
An enthalpy-based uniform lattice Boltzmann flux solver (EULBFS) is proposed in this paper for simulating liquid solidification, incorporating the effects of volume expansion and shrinkage caused by density differences between liquid and…
Parameterizing mathematical models of biological systems often requires fitting to stable periodic data. In cardiac electrophysiology this typically requires converging to a stable action potential through long simulations. We explore this…
The standard particle-in-cell algorithm suffers from grid heating. There exists a gridless alternative which bypasses the deposition step and calculates each Fourier mode of the charge density directly from the particle positions. We show…
We show that finite-range alternatives to the standard long-range BKS pair potential for silica might be used in molecular dynamics simulations. We study two such models that can be efficiently simulated since no Ewald summation is…
The quasi-2D electrostatic systems, characterized by periodicity in two dimensions with a free third dimension, have garnered significant interest in many fields. We apply the sum-of-Gaussians (SOG) approximation to the Laplace kernel,…
The effects of electromagnetic fields (EMF) have been widely debated concerning their role in chemical reactions. Reactions usually took hours or days to complete, and have been shown to happen a thousand times faster using EMF radiations.…
Constant potential molecular dynamics simulation plays important role for applications of electrochemical systems, yet the calculation of charge fluctuation on electrodes remains a computational bottleneck. We propose a highly scalable,…
The contact of solids with rough surfaces plays a fundamental role in physical phenomena such as friction, wear, sealing, and thermal transfer. However, its simulation is a challenging problem due to surface asperities covering a wide range…
In this paper we present a novel approach to FEL simulations based on the decomposition of the electromagnetic field in a finite number of radiation modes. The evolution of each mode amplitude is simply determined by energy conservation.…
The ensemble Kalman filter (EnKF) is a popular technique for performing inference in state-space models (SSMs), particularly when the dynamic process is high-dimensional. Unlike reweighting methods such as sequential Monte Carlo (SMC, i.e.…