Related papers: Adaptive coarse-graining for large-scale DEM simul…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
Discrete Element Methods (DEM), i.e.~the simulation of many rigid particles, suffer from very stiff differential equations plus multiscale challenges in space and time. The particles move smoothly through space until they interact almost…
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…
Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging…
In unresolved flow CFD-DEM simulations, the porosity values for each CFD cell are determined using a coarse-graining algorithm. While this approach enables coupled simulations of representative numbers of particles, the influence of the…
This work presents a novel framework governing the development of an efficient, accurate, and transferable coarse-grained (CG) model of a polyether material. The proposed framework combines the two fundamentally different classical…
While many diffusion models perform well when controlling particular aspects such as style, character, and interaction, they struggle with fine-grained control due to dataset limitations and intricate model architecture design. This paper…
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent…
The discrete element method (DEM) is a powerful tool for simulating granular soils, but its high computational demand often results in extended simulation times. While the effect of particle size has been extensively studied, the potential…
This paper presents an extension of the discrete element method using a phase-field formulation to incorporate grain shape and its evolution. The introduction of a phase variable enables an effective representation of grain geometry and…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…
In engineering applications snow often undergoes large and fast deformations. During these deformations the snow transforms from a sintered porous material into a granular material. In order to capture the fundamental mechanical behavior of…
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…
Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
We treat the accurate simulation of the calcination reaction in particles, where the particles are large and, thus, the inner-particle processes must be resolved. Because these processes need to be described with coupled partial…
Implicit time integration is key to robustly simulating stiff materials and large deformations, but its performance is often dominated by repeatedly solving large linear systems. Adaptive coarsening can reduce this cost by concentrating…
The aim of this paper is to propose a novel methodology to deal with micro-structural boundary conditions for the analysis of granular materials. The response of the granular assembly is modelled through the discrete element method (DEM),…