Related papers: Membrane simulation models from nm to $\mu$m scale
Immersed boundary methods are extensively used for simulations of dynamic solid objects interacting with fluids due to their computational efficiency and modelling flexibility compared to body-fitted grid methods. However, thin geometries,…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
Lipid bilayers often form high-curvature configurations due to self-assembly conditions or certain biological processes. However, particle-based simulations of lipid membranes are predominantly of flat lipid membranes because planar…
Viscosity is a key property of cell membranes that controls mobility of embedded proteins and membrane remodeling. Measuring it is challenging because existing approaches involve complex experimental designs and/or models, and the…
Bilayer lipid membranes (BLMs) are an essential component of many biological systems, forming a functional barrier between the cell and the surrounding environment. When the membrane relaxes from a structural perturbation, the dynamics of…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Morphological change of bilayer membrane in vivo is not a spontaneous procedure but modulated by various types of proteins in general. Most of these modulations are associated with the localization of related proteins in the crowded lipid…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
We preset a computational study of bending models for the curvature elasticity of lipid bilayer membranes that are relevant for simulations of vesicles and red blood cells. We compute bending energy and forces on triangulated meshes and…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Ever since the raft model for biomembranes has been proposed, the traditional view of biomembranes based on the fluid-mosaic model has been altered. In the raft model, dynamical heterogeneities in multi-component lipid bilayers play an…
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their biological activity. They also constitute a fascinating challenge for physicists, since they…
We review recent computer simulation studies of undulating lipid bilayers. Theoretical interpretations of such fluctuating membranes are most commonly based on generalized Helfrich-type elastic models, with additional contributions of local…
Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far…
We describe simulations of Proteins and artificial pseudo-molecules interacting and shaping lipid bilayer membranes. We extract protein diffusion Parameters, membrane deformation profiles and the elastic properties of the used membrane…
Over the last two decades, scientific literature has been blooming with various means of simulating epithelial cell colonies. Each of these simulations can be separated by their respective efficiency (expressed in terms of consumed…
The study of interactions between biomimetic membranes and micron-sized particles is crucial for understanding various biological processes. Here, we control microparticle spontaneous engulfment by giant lipid vesicles by tuning particle…
Molecular simulations provide a powerful means to unravel the complex relationships between network architecture and the mechanical response of polymer networks, with a particular emphasis on rupture and fracture phenomena. Although…