Related papers: A Method to Apply Piola-Kirchhoff Stress in Molecu…
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…
Atomistic computations of the Peierls stress in fcc metals are relatively scarce. By way of contrast, there are many more atomistic computations for bcc metals, as well as mixed discrete-continuum computations of the Peierls-Nabarro type…
Hard spheres are arguably one of the most fundamental model systems in soft matter physics, and hence a common topic of simulation studies. Event-driven simulation methods provide an efficient method for studying the phase behavior and…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Stress tensors are derived for the multiparticle collision dynamics algorithm, a particle-based mesoscale simulation method for fluctuating fluids, resembling those of atomistic or molecular systems. Systems with periodic boundary…
We present calculations on the deformation of two- and three-layer electret systems. The electrical field is coupled with the stress-strain equations by means of the Maxwell stress tensor. In the simulations, two-phase systems are…
Solids facing a plasma are a common situation in many astrophysical systems and laboratory setups. Moreover, many plasma technology applications rely on the control of the plasma-surface interaction. However, presently often a fundamental…
We present a systematic framework for shortening and automating molecular dynamics equilibration through improved position initialization methods and uncertainty quantification analysis, using the Yukawa one-component plasma as an exemplar…
The use of global displacement basis functions to solve boundary-value problems in linear elasticity is well established. No prior work uses a global stress tensor basis for such solutions. We present two such methods for solving stress…
We design and develop a new Particle-in-Cell (PIC) method for plasma simulations using Deep-Learning (DL) to calculate the electric field from the electron phase space. We train a Multilayer Perceptron (MLP) and a Convolutional Neural…
A numerical method is presented for first-principle simulations of charged colloidal dispersions in electrolyte solutions. Utilizing a smoothed profile for colloid-solvent boundaries, efficient mesoscopic simulations are enabled for…
We study the properties of convex functionals which have been proposed for the simulation of charged molecular systems within the Poisson-Boltzmann approximation. We consider the extent to which the functionals reproduce the true…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
A method for simulation of elastoplastic solids in multibody systems with nonsmooth and multidomain dynamics is developed. The solid is discretised into pseudo-particles using the meshfree moving least squares method. The particles carry…
This paper presents a computationally efficient method for the optimal design of silica aerogel porous material systems, balancing thermal insulation performance with mechanical stability under stress concentrations. The proposed approach…
We propose a new discretization of a mixed stress formulation of the Stokes equations. The velocity $u$ is approximated with $H(\operatorname{div})$-conforming finite elements providing exact mass conservation. While many standard methods…
A method is presented to calculate from first principles the higher-order elastic constants of a solid material. The method relies on finite strain deformations, a density functional theory approach to calculate the Cauchy stress tensor,…
The particle-in-cell (PIC) method has been widely used for plasma simulation, because of its noise-reduction capability and moderate computational cost. The immersed finite element (IFE) method is efficient for solving interface problems on…
We discuss kinetic-based particle optimization methods and variable-sample strategies for problems where the cost function represents the expected value of a random mapping. Kinetic-based optimization methods rely on a consensus mechanism…
We review existing SPH setup methods and outline their advantages, limitations and drawbacks. We present a new method for constructing initial conditions for smoothed particle hydrodynamics (SPH) simulations, which may also be of interest…