Related papers: Stabilization of Ab Initio Molecular Dynamics Simu…
Techniques for simulating molecules whose conformations satisfy constraints are presented. A method for selecting appropriate moves in Monte Carlo simulations is given. The resulting moves not only obey the constraints but also maintain…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
Recent developments in vortex particle methods for simulating three-dimensional incompressible flows are presented. A lightweight, dynamic Large-Eddy Simulation model is tested, featuring a dynamic procedure that relies solely on Lagrangian…
This work provides an efficient virtual element scheme for the modeling of nonlinear elastodynamics undergoing large deformations. The virtual element method (VEM) has been applied to various engineering problems such as elasto-plasticity,…
Variational multiscale (VMS) methods offer a robust framework for handling under-resolved flow scales without resorting to problem-specific turbulence models. Here, we propose and assess a dynamic, term-by-term VMS stabilized formulation…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
Simulations of objects with classical dynamics are in fact a particular version of discrete dynamics since almost all the classical dynamics simulations in natural science are performed with the use of the simple ''Leapfrog" or ''Verlet"…
In this paper, we propose a new formulation and a suitable finite element method for the steady coupling of viscous flow in deformable porous media using divergence-conforming filtration fluxes. The proposed method is based on the use of…
Computational formulations for large strain, polyconvex, nearly incompressible elasticity have been extensively studied, but research on enhancing solution schemes that offer better tradeoffs between accuracy, robustness, and computational…
We have recently developed a breakthrough methodology for rapidly computing entropy in both solids and liquids by integrating a multiscale entropy approach (known as zentropy theory) with molecular dynamics (MD) simulations. This approach…
In contrast to the commonly used lattice Boltzmann method, off-lattice Boltzmann methods decouple the velocity discretization from the underlying spatial grid, thus allowing for more efficient geometric representations of complex…
We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a…
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…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
A dynamical formulation of the dimer method for the determination of transition states is presented. The method is suited for ab-initio molecular dynamics using the fictitious Lagrangian formulation. The method has been applied to the…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
We investigate the theoretical foundations of the simulated tempering method and use our findings to design efficient algorithms. Employing a large deviation argument first used for replica exchange molecular dynamics [Plattner et al., J.…