Related papers: Morphogenesis by coupled regulatory networks
Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent…
We propose a dynamical neural network model with a hierarchical and modular structure. The network architecture can be derived by minimizing an energy function that is originally designed based on two kinds of neurons with quite different…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
The last decades witnessed the emergence of the field of correlated disordered media, a great challenge offering a large panel of new perspectives for applications in theoretical modelling and material fabrication. The efficient design of…
Token representations influence the efficiency and adaptability of language models, yet conventional tokenization strategies impose rigid segmentation boundaries that do not adjust dynamically to evolving contextual relationships. The…
Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of…
We analyze networked heterogeneous nonlinear systems, with diffusive coupling and interconnected over a generic static directed graph. Due to the network's hetereogeneity, complete synchronization is impossible, in general, but an emergent…
A plethora of computational models have been developed in recent decades to account for the morphogenesis of complex biological fluid networks, such as capillary beds. Contemporary adaptation models are based on optimization schemes where…
We present a model for mechanically-induced pattern formation in growing biological tissues and discuss its application to the development of leaf venation networks. Drawing an analogy with phase transitions in solids, we use a phase field…
We formulate a control system model for the distributed flow of mixtures of highly heterogeneous gases through large-scale pipeline networks with time-varying injections of constituents, withdrawals, and control actions of compressors. This…
We investigate the effect of time-dependent noise on the shape of a morphogen gradient in a developing embryo. Perturbation theory is used to calculate the deviations from deterministic behavior in a simple reaction-diffusion model of…
The co-evolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of gene regulatory network. We find that a critical state emerges spontaneously resulting from interplay between…
Cell invasion and spatial pattern formation are two distinct manifestations of cellular self-organisation in development, regeneration, and disease. Here, we develop and analyse a unified theoretical framework that links these two seemingly…
In this paper, we combine deep learning concepts and some proper orthogonal decomposition (POD) model reduction methods for predicting flow in heterogeneous porous media. Nonlinear flow dynamics is studied, where the dynamics is regarded as…
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular…
The mechanism by which cells measure the dimension of the organ in which they are embedded, and slow down their growth when the final size is reached, is a long-standing problem of developmental biology. The role of mechanics in this…
We propose a statistical model of a large random network with high connectivity in order to describe the behavior of {\it E.\,coli} cells after exposure to acute stress. The building blocks of this network are feedback cycles typical of the…
Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement of strand-displacement DNA computing, a large class of…
In this paper, we propose a projection-free power-limiting droop control for grid-connected power electronics and an associated constrained flow problem. In contrast to projection-based power-limiting droop control, the novel…
We analyze a class of chemical reaction networks under mass-action kinetics and involving multiple time-scales, whose deterministic and stochastic models display qualitative differences. The networks are inspired by gene-regulatory…