Related papers: Reaction-Diffusion Waves Coupled with Membrane Cur…
In this paper we consider mathematical modeling of the dynamics of self-organized patterning of spatially confined human embryonic stem cells (hESCs) treated with BMP4 (gastruloids) described in recent experimental works. In the first part…
The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…
Many animals have patterned fur, feathers, or scales, such as the stripes of a zebra. Turing models, or reaction-diffusion systems, are a class of mathematical models of interacting species that have been successfully used to generate…
In two-dimensional reaction-diffusion systems, local curvature perturbations in the shape of traveling waves are typically damped out and disappear in the course of time. If, however, the inhibitor diffuses much faster than the activator,…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Quantum-mechanical van der Waals dispersion interactions play an essential role for both intra-protein and protein-water interactions -- the two main driving forces for the structure and dynamics of proteins in aqueous solution. Typically,…
Pattern dynamics on curved surfaces are found everywhere in nature. The geometry of surfaces have been shown to influence dynamics and play a functional role, yet a comprehensive understanding is still elusive. Here, we report for the first…
Constructing physical models of living cells and tissues is an extremely challenging task because of the high complexities of both intra- and intercellular processes. In addition, the force that a single cell generates vanishes in total due…
Biological membranes are complex, dynamic structures essential for cellular compartmentalization, signaling, and mechanical integrity. The molecular organization of eukaryotic membranes has been extensively studied, including the lipid…
Spiral waves emerge in numerous pattern forming systems and are commonly modeled with reaction-diffusion systems. Some systems used to model biological processes, such as ion-channel models, fall under the reaction-diffusion category and…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In…
Curvature plays a central role in the proper function of many biological processes. With active matter being a standard framework for understanding many aspects of the physics of life, it is natural to ask what effect curvature has on the…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Examples of such systems include DNA-functionalized colloids as well as nanoparticles grafted with antibodies to cell membrane…
Turbulence plays a major role in shaping marine community structure as it affects organism dispersal and guides fundamental ecological interactions. Below oceanographic mesoscale dynamics, turbulence also impinges on subtle…
We study the evolution of fronts in a bistable reaction-diffusion system when the nonlinear reaction term is spatially non-homogeneous. This equation has been used to model wave propagation in various biological systems. Extending previous…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
The transformation from evanescent waves to propagation waves is the key mechanism for the realization of some super-resolution imaging methods. By using the recursive Green function and scattering-matrix theory, we investigated in details…
Turing's mechanism is often invoked to explain periodic patterns in nature, although direct experimental support is scarce. Turing patterns form in reaction-diffusion systems when the activating species diffuse much slower than the…
Collagen is the key protein of connective tissue (i.e., skin, tendons and ligaments, cartilage, among others) accounting for 25% to 35% of the whole-body protein content, and entitled of conferring mechanical stability. This protein is also…