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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…
Biomolecular condensates organize biochemical processes by spatially concentrating molecules while allowing for dynamic exchange with their surroundings. However, transport across their interface can be strongly attenuated, leading to…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
Structural causal models describe how the components of a robotic system interact. They provide both structural and functional information about the relationships that are present in the system. The structural information outlines the…
The behavior of some stochastic chemical reaction networks is largely unaffected by slight inaccuracies in reaction rates. We formalize the robustness of state probabilities to reaction rate deviations, and describe a formal connection…
Realistic examples of reaction-diffusion phenomena governing spatial and spatiotemporal pattern formation are rarely isolated systems, either chemically or thermodynamically. However, even formulations of `open' reaction-diffusion systems…
We consider biochemical reaction chains and investigate how random external fluctuations, as characterized by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of…
In this paper we present a study of pattern formation in bidimensional systems with competing short-range attractive and long-range repulsive interactions. The interaction parameters are chosen in such a way to analyse two different…
We treat a model of population dynamics in a periodic environment presenting a fast diffusion line. This phenomenon is modelled via a "road-field" system, which is a system of coupled reaction-diffusion equations set in domains of different…
We consider a model for a population in a heterogeneous environment, with logistic type local population dynamics, under the assumption that individuals can switch between two different nonzero rates of diffusion. Such switching behavior…
We study the spatial patterns formed by a system of interacting particles where the mobility of any individual is determined by the population crowding at two different spatial scales. In this way we model the behavior of some biological…
Various resonant and near-resonant patterns form in a light-sensitive Belousov-Zhabotinsky (BZ) reaction in response to a spatially-homogeneous time-periodic perturbation with light. The regions (tongues) in the forcing frequency and…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
Enhancement of the predictive power and robustness of nonlinear population dynamics models allows ecologists to make more reliable forecasts about species' long term survival. However, the limited availability of detailed ecological data,…
Many biological systems dynamically rearrange their components through a sequence of configurations in order to perform their functions. Such dynamic processes have been studied using network models that sequentially retrieve a set of…
Q-conditional symmetries (nonclassical symmetries) for a general class of two-component reaction-diffusion systems with constant diffusivities are studied. Using the recently introduced notion of Q-conditional symmetries of the first type…
Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid re-arrangements of the medium constantly change the effective diffusivity felt…
Reaction-diffusion systems have been widely used to study spatio-temporal phenomena in cell biology, such as cell polarization. Coupled bulk-surface models naturally include compartmentalization of cytosolic and membrane-bound polarity…