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In silico, cell based approaches for modeling biological morphogenesis are used to test and validate our understanding of the biological and mechanical process that are at work during the growth and the organization of multi-cell tissues.…
We develop the elastic theory for inversion-asymmetric tethered membranes and use it to identify and study their possible phases. Asymmetry in a tethered membrane causes spontaneous curvature, which in general depends upon the local…
Colloids dispersed in nematic liquid crystals form topological composites in which colloid-associated defects mediate interactions while adhering to fundamental topological constraints. Better realising the promise of such materials…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Image acquisition techniques such as micro-computed tomography are nowadays widely available. Quantitative analysis of the resulting 3D image data enables geometric characterization of the micro-structure of materials. Stochastic geometry…
Computational meshes, as a way to partition space, form the basis of much of PDE simulation technology, for instance for the finite element and finite volume discretization methods. In complex simulations, we are often driven to modify an…
This paper presents a phase-field model for simulating the three-dimensional deformation of vesicle membranes, incorporating area-difference elasticity, with constraints on bulk volume and surface area. We develop efficient numerical…
It has been considered that the effective bending rigidity of fluid membranes should be reduced by thermal undulations. However, recent thorough investigation by Pinnow and Helfrich revealed significance of measure factors for the partition…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
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)…
A method to calculate the bending rigidity $\kappa$, saddle-splay modulus $\bar{\kappa}$, and spontaneous curvature $C_0$ of a fluid membrane is proposed. Virtual work for the bending deformations into cylindrical and spherical shapes is…
Despite advances in deep learning, robustness under domain shift remains a major bottleneck in medical imaging settings. Findings on natural images suggest that deep neural models can show a strong textural bias when carrying out image…
This paper outlines the benefits of computational steering for high performance computing applications. Lattice-Boltzmann mesoscale fluid simulations of binary and ternary amphiphilic fluids in two and three dimensions are used to…
Many lipid membrane-mediated transport processes--such as mechanically-gated channel activation and solute transport--involve structural and dynamical features on membrane thickness length scales. Most existing membrane models, however,…
The plasma membrane of human red blood cells consists of a lipid bilayer attached to a regular network of underlying cytoskeletal polymers. We model this system at a dynamic coarse-grained level, treating the bilayer as an elastic sheet and…
We investigate pores in fluid membranes by molecular dynamics simulations of an amphiphile-solvent mixture, using a molecular coarse-grained model. The amphiphilic membranes self-assemble into a lamellar stack of amphiphilic bilayers…
We propose a model for membrane-cortex adhesion which couples membrane deformations, hydrodynamics and kinetics of membrane-cortex ligands. In its simplest form, the model gives explicit predictions for the critical pressure for membrane…
Encapsulation of chemicals using polymer membranes enables to control their transport and delivery for applications such as agrochemistry or detergency. To rationalize the design of polymer capsules, it is necessary to understand how the…
Even though atomistic and coarse-grained (CG) models have been used to simulate liquid nanodroplets in vapor, very few rigorous studies of the liquid-liquid interface structure are available, and most of them are limited to planar…
In this review we discuss the recent progress in the simulation of soft active matter systems and in particular the hydrodynamics of microswimmers using the method of multiparticle collision dynamics, which solves the hydrodynamic flows…