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Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…
Astrochemical modeling is needed for understanding the formation and evolution of interstellar molecules, and for extracting physical information from spectroscopic observations of interstellar clouds. The modeling usually involves handling…
The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key…
Accurate simulations of combustion phenomena require the use of detailed chemical kinetics in order to capture limit phenomena such as ignition and extinction as well as predict pollutant formation. However, the chemical kinetic models for…
Chemistry plays a key role in many astrophysical situations regulating the cooling and the thermal properties of the gas, which are relevant during gravitational collapse, the evolution of disks and the fragmentation process. In order to…
In recent years, numerical simulations have become indispensable for addressing complex astrophysical problems. The MagnetoHydroDynamics (MHD) framework represents a key tool for investigating the dynamical evolution of astrophysical…
Field emission coupled with molecular dynamics simulation (FEcMD) software package is a computational tool for studying the electron emission characteristics and the atomic structure evolution of micro- and nano-protrusions made of pure…
Hydrodynamical simulations are increasingly able to accurately model physical systems on stellar, galactic, and cosmological scales, however, the utility of these simulations is often limited by our ability to directly compare them with the…
Path-integral molecular dynamics (PIMD) simulations are crucial for accurately capturing nuclear quantum effects in materials. However, their computational intensity and reliance on multiple software packages often limit their applicability…
In this paper, we explore osmotic transport by means of molecular dynamics (MD) simulations. We first consider osmosis through a membrane, and investigate the reflection coefficient of an imperfectly semi-permeable membrane, in the dilute…
Time-to-event (survival) analysis models the time until a pre-specified event occurs. When time is measured in discrete units or rounded into intervals, standard continuous-time models can yield biased estimators. In addition, the event of…
CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfaces, as well as highly symmetric…
The simulation of high-energy physics collision events is a key element for data analysis at present and future particle accelerators. The comparison of simulation predictions to data allows looking for rare deviations that can be due to…
ergodicity is an open-source Python library for computational work on stochastic dynamics, with particular emphasis on non-ergodicity, time-average behavior, heavy-tailed processes, and decision making under uncertainty. The package brings…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
We have developed PyTIE (Python Topological Indices Expressions) which is defined as the collections of Python packages such as PyTIE D, PyTIE DS, PyTIE SMS DE, and PyTIE SMS DSE, which are open-source software packages and cross-platform…
The NTMpy code package allows for simulating the one-dimensional thermal response of multilayer samples after optical excitation, as in a typical pump-probe experiment. Several Python routines are combined and optimized to solve coupled…
We have developed an open-source software package (SedSimple) for stratigraphic forward modeling. It is aimed for use in research and education. The package uses ASCII files for input and output to facilitate understanding, debugging and…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…
Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using…