Related papers: Classical and ab initio molecular dynamic simulati…
Calculations of elastic and mechanical characteristics of non-crystalline solids are challenging due to high computation cost of $ab$ $initio$ methods and low accuracy of empirical potentials. We propose a computational technique towards…
Classical molecular dynamics (MD) simulations will be able to reach sampling in the second timescale within five years, producing petabytes of simulation data at current force field accuracy. Notwithstanding this, MD will still be in the…
We provide a methodology for generating interatomic potentials for use in classical molecular dynamics simulations of atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high energy…
In studying solidification process by simulations on the atomic scale, the modeling of crystal nucleation or amorphisation requires the construction of interatomic interactions that are able to reproduce the properties of both the solid and…
We investigate properties of dense suspensions and sediments of small spherical silt particles by means of a combined Molecular Dynamics (MD) and Stochastic Rotation Dynamics (SRD) simulation. We include van der Waals and effective…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
We present results from the molecular dynamics (MD) simulation of surface-directed spinodal decomposition (SDSD) in binary fluid mixtures ($A+B$) with off-critical compositions. The aim is to elucidate the role of composition ratio in the…
We introduce a novel concept, the minimal molecular surface (MMS), as a new paradigm for the theoretical modeling of biomolecule-solvent interfaces. When a less polar macromolecule is immersed in a polar environment, the surface free energy…
Owing to the advances in computational techniques and the increase in computational power, atomistic simulations of materials can simulate large systems with higher accuracy. Complex phenomena can be observed in such state-of-the-art…
In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics.…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
The theory underlying the Car-Parrinello extended-lagrangian approach to {\em ab initio} molecular dynamics (CPMD) is reviewed and reexamined using 'heavy' ice as a test system. It is emphasized that the adiabatic decoupling in CPMD is not…
Porous structures are intricate solid materials with numerous small pores, extensively used in fields like medicine, chemical engineering, and aerospace. However, the design of such structures using computer-aided tools is a time-consuming…
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…
Brownian dynamics of colloidal particles on complex surfaces has found important applications in diverse physical, chemical and biological processes. However, current Brownian dynamics simulation algorithms mostly work for relatively simple…
A well-known drawback of state-of-the-art machine-learning interatomic potentials is their poor ability to extrapolate beyond the training domain. For small-scale problems with tens to hundreds of atoms this can be solved by using active…
We report a new Quantum Mechanical/Molecular Dynamics (QM/MD) simulation loop to model the coupling between the electron and atom dynamics in solid/liquid interfacial systems. The method can describe simultaneously both the quantum…
We present the results of a molecular dynamics computer simulation in which we investigate the dynamics of silica. By considering different system sizes, we show that in simulations of the dynamics of this strong glass former surprisingly…
Amorphous silicon nitride (a-SiN) is a material which has found wide application due to its excellent mechanical and electrical properties. Despite the significant effort devoted in understanding how the microscopic structure influences the…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…