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In recent years, machine learning interatomic potentials (MLIPs) have attracted significant attention as a method that enables large-scale, long-time atomistic simulations while maintaining accuracy comparable to electronic structure…

Identification of the parameters of stable linear dynamical systems is a well-studied problem in the literature, both in the low and high-dimensional settings. However, there are hardly any results for the unstable case, especially…

This is a technical report that extends and clarifies the results presented in [1]. The model identification problem for asymptotically stable linear time invariant systems is considered. The system output is affected by an additive noise…

We derive a new criterion for estimating characteristic dynamical timescales in N-body simulations. The criterion uses the second, third, and fourth derivatives of particle positions: acceleration, jerk, and snap. It can be used for…

Feynman path integrals (PIs) have found many uses in approximate quantum dynamics methods that are able to efficiently calculate real-time quantum correlation functions. The PIs typically take the form of discrete imaginary time slices over…

We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…

Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…

Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…

We simulate the dynamics, including laser cooling, of 3D ion crystals confined in a Penning trap using a newly developed molecular dynamics-like code. The numerical integration of the ions' equations of motion is accelerated using the fast…

Large clouds of atoms in a magneto-optical trap (MOT) are known to exhibit spatiotemporal instabilities when the frequency of the trapping lasers comes close to the atomic resonance. Such instabilities possess similarities with stars and…

Accurate prediction of energy and forces for 3D molecular systems is one of fundamental challenges at the core of AI for Science applications. Many powerful and data-efficient neural networks predict molecular energies and forces from…

Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…

Discrete Element Methods (DEM), i.e.~the simulation of many rigid particles, suffer from very stiff differential equations plus multiscale challenges in space and time. The particles move smoothly through space until they interact almost…

With the aim of establishing a criterion for identifying when a lipid bilayer has reached steady state using the molecular dynamics simulation technique, lipid bilayers of different composition in their liquid crystalline phase were…

An investigation to optimize the application of the third-generation charge optimized many-body (COMB3) interatomic potential and associated input parameters was carried out through the study of solid-liquid interactions in classical…

Motivated by the very low diffusivity recently found in ab initio simulations of liquid water, we have studied its dependence with temperature, system size, and duration of the simulations. We use ab initio molecular dynamics (AIMD),…

Integrating out fast degrees of freedom is known to yield, to a good approximation, memory-less, i.e. Markovian, dynamics. In the presence of such a time-scale separation local detailed balance is believed to emerge and to guarantee…

The experimental results relevant for the understanding of the microscopic dynamics in liquid metals are reviewed, with special regards to the ones achieved in the last two decades. Inelastic Neutron Scattering played a major role since the…

A hierarchical (triple scale) simulation methodology is presented for the prediction of the dynamical and rheological properties of high molecular weight entangled polymer melts. The methodology consists of atomistic, moderately…

Multiparticle collision dynamics (MPCD) enables to simulate fluid dynamics including both hydrodynamics and thermal fluctuations. Its main use concerns complex fluids, where the solvent interacts with concentrated solutes, may they be…