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Constant potential methods (CPM) enable computationally efficient simulations of the solid-liquid interface at conducting electrodes in molecular dynamics (MD). They have been successfully used, for example, to realistically model the…
We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense…
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled…
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…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…
Free energy calculation is critical in predictive tasks such as protein folding, docking and design. However, rigorous calculation of free energy change is prohibitively expensive in these practical applications. The minimum potential…
The hybrid method combining particle-in-cell and magnetohydrodynamics can be used to study the interaction between energetic particles and global plasma modes. In this paper we introduce the M3D-C1-K code, which is developed based on the…
Classical density-functional theory is the most direct approach to equilibrium structures and free energies of inhomogeneous liquids, but requires the construction of an approximate free-energy functional for each liquid of interest. We…
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…
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are…
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…
The implementation of a new particle module describing the physics of dust grains coupled to the gas via drag forces is the subject of this work. The proposed particle-gas hybrid scheme has been designed to work in Cartesian as well as in…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
Numerical simulation of plasma discharges is often performed by models developed in-house and coupling externally and separately written codes. The MOOSE (Multiphysics Object Oriented Simulation Environment) framework provides tools for…
The interfacial free energy between a crystal and a fluid, {\gamma} cf, is a highly relevant parameter in phenomena such as wetting or crystal nucleation and growth. Due to the difficulty of measuring {\gamma} cf experimentally, computer…
Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in…
Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis of MD trajectories often relies on the choice of collective…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…
Binding processes are difficult to sample with molecular-dynamics (MD) simulations. In particular, the state space exploration is often incomplete. Evaluating the molecular interaction energy on a grid circumvents this problem but is…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…