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We propose an approach that links density functional theory (DFT) and molecular dynamics (MD) simulation to study fluid behavior in nanopores in contact with bulk (macropores). It consists of two principal steps. First, the theoretical…
A computational approach has been developed for the analysis of the properties of 3D dislocation substructures generated by the vector density continuum dislocation dynamics (CDD), within the framework of crystal plasticity. In the CDD…
Path Integral Molecular Dynamics (PIMD) is a well established simulation technique to compute exact equilibrium properties for a quantum system using classical trajectories in an extended phase space. Standard PIMD simulations are…
We present a flexible, open-source Python package for the accurate simulation of the $z$-propagation dynamics of ultrashort optical pulses in nonlinear waveguides, especially valid for few-cycle pulses and their interaction. The simulation…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure.…
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a significant role but is not the primary interest. Such methods generally…
We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
We present TTCF4LAMMPS, a toolkit for performing non-equilibrium molecular dynamics (NEMD) simulations to study fluid behaviour at low shear rates using the LAMMPS software. By combining direct NEMD simulations and the transient-time…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow…
Acid-base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in many fields, from biochemistry to industrial catalysis. Unfortunately, experiments only give limited information without much insight into the…
DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the…
Recent advances in quantum simulators permit unitary evolution interspersed with locally resolved mid-circuit measurements. This paves the way for the observation of large-scale space-time structures in quantum trajectories and opens a…
The ensemble empirical mode decomposition (EEMD) and its complete variant (CEEMDAN) are adaptive, noise-assisted data analysis methods that improve on the ordinary empirical mode decomposition (EMD). All these methods decompose possibly…
Dissipative particle dynamics (DPD) is a relatively new technique which has proved successful in the simulation of complex fluids. We caution that for the equilibrium achieved by the DPD simulation of a simple fluid the temperature depends…
Ab initio Born-Oppenheimer molecular dynamics (AIMD) is a valuable method for simulating physico-chemical processes of complex systems, including reactive systems, and for training machine learning models and force fields. Speed and…
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of…