Related papers: Simulating Organogenesis in COMSOL Multiphysics: T…
We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case…
Cells often migrate on curved surfaces inside the body, such as curved tissues, blood vessels or highly curved protrusions of other cells. Recent \textit{in-vitro} experiments provide clear evidence that motile cells are affected by the…
Coordinated cellular movements are key processes in tissue morphogenesis. Using a cell-based modeling approach we study the dynamics of epithelial layers lining surfaces with constant and varying curvature. We demonstrate that extrinsic…
Intracellular organelles are subject to a steady flux of lipids and proteins through active, energy consuming transport processes. Active fission and fusion are promoted by GTPases, e.g., Arf-Coatamer and the Rab-Snare complexes, which both…
In the absence of environmental cues, a migrating cell performs an isotropic random motion. Recently, the breaking of this isotropy has been observed when cells move in the presence of asymmetric adhesive patterns. However, up to now the…
We present a coarse-grained C$\alpha$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of…
Organoids are complex, three dimensional, self-organizing cell cultures which manifest organ-like features and represent a powerful platform for studying human disease and developing treatment options. Organoid development is characterized…
A number of biological processes, such as embryo development, cancer metastasis or wound healing, rely on cells moving in concert. The mechanisms leading to the emergence of coordinated motion remain however largely unexplored. Although…
Since its introduction in 1952, Turing's (pre-)pattern theory ("the chemical basis of morphogenesis") has been widely applied to a number of areas in developmental biology. The related pattern formation models normally comprise a system of…
We describe a hybrid agent-based model and simulation of urban morphogenesis. It consists of a cellular automata grid coupled to a dynamic network topology. The inherently heterogeneous properties of urban structure and function are taken…
In this article, we continue our mathematical study of organic solar cells (OSCs) and propose a two-scale (micro- and macro-scale) model of heterojunction OSCs with interface geometries characterized by an arbitrarily complex morphology.…
Confluent cell monolayers and epithelia tissues show remarkable patterns and correlations in structural arrangements and actively-driven collective flows. We simulate these properties using multiphase field models. The models are based on…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
The shape that stem cells reach at the end of adhesion process influences their differentiation. Rearrangement of cytoskeleton and modification of intracellular tension may activate mechanotransduction pathways controlling cell commitment.…
Morphogenetic dynamics of tissue sheets require coordinated cell shape changes regulated by global patterning of mechanical forces. Inspired by such biological phenomena, we propose a minimal mechanochemical model based on the notion that…
The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…
The advancement of human healthspan and bioengineering relies heavily on predicting the behavior of complex biological systems. While high-throughput multiomics data is becoming increasingly abundant, converting this data into actionable…
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 study of organoids, artificially grown cell aggregates with the functionality and small-scale anatomy of real organs, is one of the most active areas of research in biology and biophysics, yet the basic physical origins of their…
How pattern and form are generated in a reproducible manner during embryogenesis remains poorly understood. Intestinal organoid morphogenesis involves a number of mechanochemical regulators, including cell-type specific cytoskeletal forces…