Related papers: Parameter-robust preconditioners for a cell-by-cel…

Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…

We present a novel platform for the large-scale simulation of fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space. One of the main motivations for this work is to study the dynamics of fiber…

The preconditioned iterative solution of large-scale saddle-point systems is of great importance in numerous application areas, many of them involving partial differential equations. Robustness with respect to certain problem parameters is…

Membrane computing is a well-established and successful research field which belongs to the more general area of molecular computing. Membrane computing aims at defining parallel and non-deterministic computing models, called membrane…

The structural diversity of the solute molecules involved in biomolecular processes necessitates the characterization of the forces between charged macromolecules beyond the point-ion description. From the field theoretic partition function…

In biological tissues, it is now well-understood that mechanical cues are a powerful mechanism for pattern regulation. While much work has focused on interactions between cells and external substrates, recent experiments suggest that cell…

Robotic systems operating in unstructured environments require the ability to switch between compliant and rigid states to perform diverse tasks such as adaptive grasping, high-force manipulation, shape holding, and navigation in…

A preconditioning strategy is proposed for the iterative solve of large numbers of linear systems with parameter-dependent matrix and right-hand side which arise during the computation of solution statistics of stochastic elliptic partial…

Understanding dynamic and complex interaction of biological membranes with extracellular matrices plays a crucial role in controlling a variety of cell behavior and functions, from cell adhesion and growth to signaling and differentiation.…

Cell blebs are protrusions of the cell membrane and can be instrumental for cell migration. We derive a continuum model for the mechanical and geometrical aspects of the onset of blebbing in terms of a force balance. It is abstract and…

The permeability is one of the most fundamental transport properties in soft matter physics, material engineering, and nanofluidics. Here we report by means of Langevin simulations of ideal penetrants in a nanoscale membrane made of a fixed…

Neural preconditioners for real-time physics simulation offer promising data-driven priors, but they often fail to capture long-range couplings efficiently because they inherit local message passing or sparse-operator access patterns. We…

As an example for the interplay of structure, dynamics, and phase behavior of macromolecular systems, this article focuses on the problem of bottle-brush polymers with either rigid or flexible backbones. On a polymer with chain length…

Swimming cells and microorganisms must often move though complex fluids that contain an immersed microstructure such as polymer molecules, or filaments. In many important biological processes, such as mammalian reproduction and bacterial…

Lipid membranes, the barrier defining living cells and many of their sub-compartments, bind to a wide variety of nano- and micro-meter sized objects. In the presence of strong adhesive forces, membranes can strongly deform and wrap the…

Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet, no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such…

Many applications involving porous media--notably reservoir engineering and geologic applications--involve tight coupling between multiphase fluid flow, transport, and poromechanical deformation. While numerical models for these processes…

Several cellular activities, such as directed cell migration, are coordinated by an intricate network of biochemical reactions which lead to a polarised state of the cell, in which cellular symmetry is broken, causing the cell to have a…

We propose and analyze a mathematical model of the mechanics of gels, consisting of the laws of balance of mass and linear momentum. We consider a gel to be an immiscible and incompressible mixture of a nonlinearly elastic polymer and a…

We derive parameter-robust quasi-optimal error estimates for mixed finite element methods for the nonlinear Darcy--Forchheimer equations with mixed boundary conditions. Using the framework of operator preconditioning, we also design…