Related papers: Tungsten migration energy barriers for surface dif…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
Monte Carlo methods are state-of-the-art when it comes to dosimetric computations in radiotherapy. However, the execution time of these methods suffers in high-collisional regimes. We address this problem by introducing a kinetic-diffusion…
Purpose: Very fast Monte Carlo (MC) simulations of proton transport have been implemented recently on GPUs. However, these usually use simplified models for non-elastic (NE) proton-nucleus interactions. Our primary goal is to build a…
Predicting diffusion in chemically complex alloys remains challenging due to the strong dependence of migration barriers on local atomic environments. Here, we develop a first-principles-informed framework that directly learns…
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…
The application of a bundling technique to model the diverse charge states of tungsten impurity species in total-f gyrokinetic simulations is demonstrated. The gyrokinetic bundling method strategically groups tungsten ions of similar…
An efficient method for the simulation of strained heteroepitaxial growth with intermixing using kinetic Monte Carlo is presented. The model used is based on a solid-on-solid bond counting formulation in which elastic effects are…
A hybrid Monte Carlo (HMC) approach is employed to quantify the influence of inelastic deformation on the microstructural evolution of polycrystalline materials. This approach couples a time explicit material point method (MPM) for…
Popular methods for identifying transition paths between energy minima, such as the nudged elastic band and string methods, typically do not incorporate potential energy curvature information, leading to slow relaxation to the minimum…
The evaluation of nucleation rates from molecular dynamics trajectories is hampered by the slow nucleation time scale and impact of finite size effects. Here, we show that accurate nucleation rates can be obtained in a very general fashion…
We propose enforcing constraints on Model-Based Diffusion by introducing emerging barrier functions inspired by interior point methods. We demonstrate that the standard Model-Based Diffusion algorithm can lead to catastrophic performance…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
Electromigration-induced flow of islands and voids on the Cu(001) surface is studied at the atomic scale. The basic drift mechanisms are identified using a complete set of energy barriers for adatom hopping on the Cu(001) surface, combined…
Spontaneous transport barrier generation at the edge of a magnetically confined plasma is investigated. To this end, a model of electrostatic turbulence in three-dimensional geometry is extended to account for the impact of friction between…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…
Using a combination of kinetic Activation Relaxation Technique with empirical potential and ab initio based climbing image nudged elastic band method, we perform an extensive search of the migration and rotation paths of the most stable…
We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are…
We present a collision model for phase-resolved Direct Numerical Simulations of sediment transport that couple the fluid and particles by the Immersed Boundary Method. Typically, a contact model for these types of simulations comprises a…
The dynamics of the discrete Gaussian model for the surface of a crystal deposited on a disordered substrate is investigated by Monte Carlo simulations. The mobility of the growing surface was studied as a function of a small driving force…
The first off-lattice Monte Carlo kinetics model of interstellar dust-grain surface chemistry is presented. The positions of all surface particles are determined explicitly, according to the local potential minima resulting from the…