Related papers: Simulating Organogenesis in COMSOL Multiphysics: T…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
The actin cytoskeleton of cells is in continuous motion due to both polymerization of new filaments and their contraction by myosin II molecular motors. Through adhesion to the substrate, such intracellular flow can be converted into cell…
Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behaviour of single cells, we use extensive Monte Carlo simulations to predict non-trivial…
The phenomenon of cell sorting/segregation, by which cells organise spatially into clusters of specific cell type or function, is essential for tissue morphogenesis. This self-organization process involves an interplay between mechanical,…
The Transformer architecture has revolutionized artificial intelligence, yet a principled theoretical understanding of its internal mechanisms remains elusive. This paper introduces a novel analytical framework that reconceptualizes the…
Amoeboid cell motility is relevant in a wide variety of biomedical applications such as wound healing, cancer metastasis, and embryonic morphogenesis. It is characterized by pronounced changes of the cell shape associated with expansions…
Self-organization is a fundamental process of complex biological systems, particularly during the early stages of development. In the mammalian embryo, blastocyst formation exemplifies a self-organized system, involving the correct…
Suspensions of swimming micro-organisms provide examples of coordinated active dynamics. That has stimulated the study of a phenomenological theory combining synchronization and polar order in active matter. Here, we consider another…
Partial differential equations (PDEs) govern a wide range of physical systems, and recent multimodal foundation models have shown promise for learning PDE solution operators across diverse equation families. However, existing multi-operator…
In this work we approach cell migration under a large-scale assumption, so that the system reduces to a particle in motion. Unlike classical particle models, the cell displacement results from its internal activity: the cell velocity is a…
We provide a review of recent advancements in nonlocal continuous models for migration, mainly from the perspective of its involvement in embryonal development and cancer invasion. Particular emphasis is placed on spatial nonlocality…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
In this paper, phase field models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic…
Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that…
The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the…
We propose a PDE-ODE model for tissue regeneration, obtained by parabolic upscaling from kinetic transport equations written for the mesoscopic densities of mesenchymal stem cells and chondrocytes which evolve in an artificial scaffold…
We present PDE-FM, a modular foundation model for physics-informed machine learning that unifies spatial, spectral, and temporal reasoning across heterogeneous partial differential equation (PDE) systems. PDE-FM combines spatial-spectral…
We show that when cells communicate by contact-mediated interactions, heterogeneity in cell shapes and sizes leads to qualitatively distinct collective behavior in the tissue. For inter-cellular coupling that implements lateral inhibition,…
Diffusion models have emerged as powerful generative tools for modeling complex data distributions, yet their purely data-driven nature limits applicability in practical engineering and scientific problems where physical laws need to be…
Microelectronic morphogenesis is the creation and maintenance of complex functional structures by microelectronic information within shape-changing materials. Only recently has in-built information technology begun to be used to reshape…