Related papers: A computational framework for modeling cell-matrix…
The shoulder joint is one of the functionally and anatomically most sophisticated articular systems in the human body. Both complex movement patterns and the stabilization of the highly mobile joint rely on intricate three-dimensional…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
We investigate the mechanical interplay between the spatial organization of the actin cytoskeleton and the shape of animal cells adhering on micropillar arrays. Using a combination of analytical work, computer simulations and in vitro…
A living cell actively generates traction forces on its environment with its actin cytoskeleton. These forces deform the cell elastic substrate which, in turn, affects the traction forces exerted by the cell and can consequently modify the…
The mechanics of animal cells is strongly determined by stress fibers, which are contractile filament bundles that form dynamically in response to extracellular cues. Stress fibers allow the cell to adapt its mechanics to environmental…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
With this contribution, we give a complete and comprehensive framework for modeling the dynamics of complex mechanical structures as port-Hamiltonian systems. This is motivated by research on the potential of lightweight construction using…
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
Contractile biopolymer networks, such as the actomyosin meshwork of animal cells, are ubiquitous in living organisms. The active gel theory, which provides the thermodynamic framework for these materials, has been mostly used in conjunction…
This paper introduces a model for the mechanical response of anisotropic soft materials undergoing large inelastic deformations. The composite is constituted by a soft isotropic matrix reinforced with stiff fibres, that can evolve…
The measurement of cellular traction forces on soft elastic substrates has become a standard tool for many labs working on mechanobiology. Here we review the basic principles and different variants of this approach. In general, the…
Incompressibility, nonlinear deformation under stress and viscoelasticity are the fingerprint of soft tissue mechanical behavior. In order to model soft tissues appropriately, we must pursue to complete these requirements. In this work we…
While mechanobiology has demonstrated that precise control over mechanical properties at the whole-cell level is crucial for many biological functions, comparatively little attention has been paid to the intracellular mechanical properties.…
Small magnetic particles placed in a relatively soft polymer (with elastic modulus E ~ 10-100 kPa) are magnetically soft elastomers. The external magnetic field acts on each particle which leads to microscopic deformation of the material…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
We propose a general framework to extract microscopic interactions from raw configurations with deep neural networks. The approach replaces the modeling Hamiltonian by the neural networks, in which the interaction is encoded. It can be…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
A network of semiflexible biopolymers, known as the cytoskeleton, and molecular motors play fundamental mechanical roles in cellular activities. The cytoskeletal response to forces generated by molecular motors is profoundly linked to…