Related papers: An introduction to classical molecular dynamics si…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Computational physics is an important tool for analysing, verifying, and -- at times -- replacing physical experiments. Nevertheless, simulating quantum systems and analysing quantum data has so far resisted an efficient classical treatment…
We have adapted classical molecular dynamics to study the structural and dynamical properties of amorphous silica surfaces. Concerning the structure, the density profile exhibits oscillations perpendicularly to the surface as observed in…
This manuscript aims to illustrate a quantum-classical dissipative theory (suited to be converted to effective algorithms for numerical simulations) within the long-term project of studying molecular processes in the brain. Other…
End-to-end learning of dynamical systems with black-box models, such as neural ordinary differential equations (ODEs), provides a flexible framework for learning dynamics from data without prescribing a mathematical model for the dynamics.…
A general method is discussed to obtain Markovian master equations which describe the interaction with the environment in a microscopic and non-perturbative fashion. It is based on combining time-dependent scattering theory with the concept…
Studying chemical reactions, particularly in the gas phase, relies heavily on computing scattering matrix elements. These elements are essential for characterizing molecular reactions and accurately determining reaction probabilities.…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
We study the diffusion of monochromatic classical waves in a disordered acoustic medium by scattering theory. In order to avoid artifacts associated with mathematical point scatterers, we model the randomness by small but finite insertions.…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
An open source software package for modelling thermal neutron transport is presented. The code facilitates Monte Carlo-based transport simulations and focuses in the initial release on interactions in both mosaic single crystals as well as…
Born-Oppenheimer dynamics is shown to provide an accurate approximation of time-independent Schr\"odinger observables for a molecular system with an electron spectral gap, in the limit of large ratio of nuclei and electron masses, without…
Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical…
The rotational dynamics of particles subject to external illumination is found to produce light amplification and inelastic scattering at high rotation velocities. Light emission at frequencies shifted with respect to the incident light by…
A practical introduction to stochastic modelling of reaction-diffusion processes is presented. No prior knowledge of stochastic simulations is assumed. The methods are explained using illustrative examples. The article starts with the…
Many physical, chemical and biological systems can be modeled by means of random-frequency harmonic oscillator systems. Even though the noise-free evolution of harmonic oscillator systems can be easily implemented, the way to experimentally…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Elastic wave propagation is studied in a heterogeneous 2-D medium consisting of an elastic matrix containing randomly distributed circular elastic inclusions. The aim of this study is to determine the effective wavenumbers when the incident…
A second order classical perturbation theory is developed and applied to elastic atom corrugated surface scattering. The resulting theory accounts for experimentally observed asymmetry in the final angular distributions. These include…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…