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To evaluate electrostatics interactions, Molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM)…

We investigate the properties of the stochastic Gross-Pitaevskii equation describing a condensate interacting with a stationary thermal cloud derived by Gardiner and coworkers. We find the appropriate Ehrenfest relations for the SGPE,…

We examine the challenge of performing accurate electronic structure calculations at high pressures by comparing the results of all-electron full potential linearized augmented-plane-wave calculations with those of the projector augmented…

Extended Lagrangian Born-Oppenheimer molecular dynamics (XL-BOMD) [Phys. Rev. Lett. vol. 100, 123004 (2008)] is combined with Kohn-Sham density functional theory (DFT) using a DFT+U correction based on the Hubbard model. This combined…

We present entropy-limited hydrodynamics (ELH): a new approach for the computation of numerical fluxes arising in the discretization of hyperbolic equations in conservation form. ELH is based on the hybridisation of an unfiltered high-order…

Using a time-dependent approach the analysis and optimization of a planar FEL-amplifier with an axial magnetic field and an irregular waveguide is performed. By applying methods of nonlinear dynamics three-dimensional equations of motion…

Using the information theory, this study provides insights into how the construction of latent space of autoencoder (AE) using deep neural network (DNN) training finds a smooth low-dimensional manifold in the stiff dynamical system. Our…

Adiabatic mixed quantum/classical molecular dynamics simulations were used to generate snapshots of the hydrated electron (e-) in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the e- were…

Efficient hybrid DFT simulations of solid state materials would be extremely beneficial for computational chemistry and materials science, but is presently bottlenecked by difficulties in computing Hartree-Fock (HF) exchange with plane wave…

Extended Lagrangian Born-Oppenheimer molecular dynamics [{\em Phys.\ Rev.\ Lett.\ } {\bf 2008}, {\em 100}, 123004] is presented for Hartree-Fock theory, where the extended electronic degrees of freedom are represented by a density matrix,…

The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy (cryo-EM), require freezing the sample, which limits the…

Conventional theoretical and computational approaches to fully coupled quantum molecular dynamics, i.e. when both the electrons and nuclei are treated as quantum-mechanical particles, are impractical for all but the smallest chemical…

To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist to obtain the thermodynamic functions for such systems. But…

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory (DFT) calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane…

The space-time adaptive ADER-DG finite element method with LST-DG predictor and a posteriori sub-cell ADER-WENO finite-volume limiting was used for simulation of multidimensional reacting flows with detonation waves. The presented numerical…

Stochastic and mixed stochastic-deterministic density functional theory (DFT) are promising new approaches for the calculation of the equation-of-state and transport properties in materials under extreme conditions. In the intermediate warm…

Predictive simulations of complex systems are essential for applications ranging from weather forecasting to drug design. The veracity of these predictions hinges on their capacity to capture the effective system dynamics. Massively…

We present an implementation of the multiconfiguration time-dependent Hartree-Fock method based on the adaptive finite element method for molecules under intense laser pulses. For efficient simulations, orbital functions are propagated by a…

We describe a fast parallel iterative method for computing molecular absorption spectra within TDDFT linear response and using the LCAO method. We use a local basis of "dominant products" to parametrize the space of orbital products that…

Recent interest in structure solution and refinement using electron diffraction (ED) has been fuelled by its inherent advantages when applied to crystals of sub-micron size, as well as a better sensitivity to light elements. Currently, data…