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The microscopic structure of a plant cell wall is given by cellulose microfibrils embedded in a cell wall matrix. In this paper we consider a microscopic model for interactions between viscoelastic deformations of a plant cell wall and…
In Part I of this article we have developed a novel mechanobiological model of a Tissue Engineering process that accounts for the mechanisms through which an isotropic or anisotropic adherence condition regulates the active functions of the…
We introduce a general, efficient method to completely describe the topology of individual grains, bubbles, and cells in three-dimensional polycrystals, foams, and other multicellular microstructures. This approach is applied to a pair of…
The motion of cells in tissues is an ubiquitous phenomenon. In particular, in monolayered cell colonies in vitro, pronounced collective behavior with swirl-like motion has been observed deep within a cell colony, while at the same time, the…
We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions…
Biological systems exhibit processes on a wide range of time and length scales. This work demonstrates that models, wherein the interaction between system constituents is captured by algebraic operations, inherently allow for successive…
We develop a phenomenological coarse--graining procedure for activity in a large network of neurons, and apply this to recordings from a population of 1000+ cells in the hippocampus. Distributions of coarse--grained variables seem to…
We develop coarse-grained particle approaches for studying the elastic mechanics of vesicles with heterogeneous membranes having phase-separated domains. We perform simulations both of passive shape fluctuations and of active systems where…
We investigate the properties of membranes under tension by Monte-Carlo simulations of a generic coarse-grained model for lipid bilayers. We give a comprising overview of the behavior of several membrane characteristics, such as the area…
Although tissues are usually studied in isolation, this situation rarely occurs in biology, as cells, tissues, and organs, coexist and interact across scales to determine both shape and function. Here, we take a quantitative approach…
In biology, cells undergo deformations under the action of flow caused by the fluid surrounding them. These flows lead to shape changes and instabilities that have been explored in detail for single component vesicles. However, cell…
We present a stochastic phase-field model for multicomponent lipid bilayers that explicitly accounts for the quasi-two-dimensional hydrodynamic environment unique to a thin fluid membrane immersed in aqueous solution. Dynamics over a wide…
We propose a simple continuum model to interpret the shearing motion of dense, dry and cohesion-less granular media. Compressibility, dilatancy and Coulomb-like friction are the three basic ingredients. The granular stress is split into a…
Granular materials segregate by size under shear, and the ability to quantitatively predict the time required to achieve complete segregation is a key test of our understanding of the segregation process. In this paper, we apply the…
A molecular-dynamics type simulation method, which is suitable for investigating the dewetting dynamics of thin and viscous liquid layers, is discussed. The efficiency of the method is exemplified by studying a two-parameter depinning-like…
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…
Cell-based, mathematical modeling of collective cell behavior has become a prominent tool in developmental biology. Cell-based models represent individual cells as single particles or as sets of interconnected particles, and predict the…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Epithelial tissues act as barriers and, therefore, must repair themselves, respond to environmental changes and grow without compromising their integrity. Consequently, they exhibit complex viscoelastic rheological behavior where…
Understanding the structure and dynamics of liquids is pivotal for the study of larger spatiotemporal processes, especially in glass-forming materials at low temperatures. Density scaling, observed in many molecular systems through…