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Continuum Monte-Carlo simulations at constant pressure are performed on short chain molecules at surfaces. The rodlike chains, consisting of seven effective monomers, are attached at one end to a flat twodimensional substrate. It is found…

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…

Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…

The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We…

We compare two recently developed mesoscale models of binary immiscible and ternary amphiphilic fluids. We describe and compare the algorithms in detail and discuss their stability properties. The simulation results for the cases of…

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed…

Gaining access to the cell interior is fundamental for many applications, such as electrical recording, drug and biomolecular delivery. A very promising technique consists of culturing cells on nano/micro pillars. The tight adhesion and…

We introduce a novel masked pre-training technique for graph neural networks (GNNs) applied to computational fluid dynamics (CFD) problems. By randomly masking up to 40\% of input mesh nodes during pre-training, we force the model to learn…

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…

One of the current challenges in physically-based simulations, and, more specifically, fluid simulations, is to produce visually appealing results at interactive rates, capable of being used in multiple forms of media. In recent times, a…

Creating realistic droplet simulations and animations has long been a formidable challenge for researchers and developers due to the inherent complexity of fluid dynamics. Achieving lifelike droplet splash simulations while managing…

We study the shape, elasticity and fluctuations of the recently predicted (cond-mat/9510172) and subsequently observed (in numerical simulations) (cond-mat/9705059) tubule phase of anisotropic membranes, as well as the phase transitions…

Simulating liquid water to an accuracy that matches its wealth of available experimental data requires both precise electronic structure methods and reliable sampling of nuclear (quantum) motion. This is challenging because applying the…

An important challenge in robotics is understanding the interactions between robots and deformable terrains that consist of granular material. Granular flows and their interactions with rigid bodies still pose several open questions. A…

Gas transport across cell membrane is a very important process in biochemistry which is essential for many crucial tasks, including cell respiration pH regulation in the cell. In the late 1990's, the suggestion that gasses are transported…

We study the elastic response of bilayer membranes with fixed projected area to both stretching and shape deformations. A surface tension is associated to each of these deformations. By using model amphiphilic membranes and computer…

Here we present first results simulating plasma filaments in non-axisymmetric geometries, using a fluid turbulence extension of the \boutxx~framework. This is made possible by the implementation of the Flux Coordinate Independent scheme for…

We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…

The use of excessively long timesteps in dissipative particle dynamics simulations may produce simulation artifacts due to the generation of configurations which are not representative of the desired canonical ensemble. The configurational…

Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…