Related papers: Morphogenesis by coupled regulatory networks
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…
According to empirical observations, some pattern formation phenomena in driven many-particle systems are more pronounced in the presence of a certain noise level. We investigate this phenomenon of fluctuation-driven ordering with a…
We propose a mechanism for mechanical regulation at the membrane of living cells, based on the exchange of membrane area between the cell membrane and a membrane reservoir. The reservoir is composed of invaginated membrane microdomains…
We consider a network of randomly coupled rate-based neurons influenced by external and internal noise. We derive a second-order stochastic mean-field model for the network dynamics and use it to analyze the stability and bifurcations in…
The ability to effectively control brain dynamics holds great promise for the enhancement of cognitive function in humans, and the betterment of their quality of life. Yet, successfully controlling dynamics in neural systems is challenging,…
The propagation of noise through parallel regulatory pathways is a characteristic feature of feed-forward loops in genetic networks. Although the contributions of the direct and indirect regulatory pathways of feed-forward loops to output…
Synthetic biology is an interdisciplinary field aiming to design biochemical systems with desired behaviors. To this end, molecular controllers have been developed which, when embedded into a pre-existing ambient biochemical network,…
We present a general computational theory of stem cell networks and their developmental dynamics. Stem cell networks are special cases of developmental control networks. Our theory generates a natural classification of all possible stem…
In biological systems, the growth of cells, tissues, and organs is influenced by mechanical cues. Locally, cell growth leads to a mechanically heterogeneous environment as cells pull and push their neighbors in a cell network. Despite this…
We consider a network of identical, first-order linear systems, and investigate how replacing a subset of the systems composing the network with higher-order ones, either taken to be generic or specifically designed, may affect its…
Recent experiments have shown that the spontaneous activity of young dissociated neuronal cultures can be described as a process of highly inhomogeneous nucleation and front propagation due to the localization of noise activity, i.e., noise…
Even under constant external conditions, the expression levels of genes fluctuate. Much emphasis has been placed on the components of this noise that are due to randomness in transcription and translation; here we analyze the role of noise…
Robustness to mutations and noise has been shown to evolve through stabilizing selection for optimal phenotypes in model gene regulatory networks. The ability to evolve robust mutants is known to depend on the network architecture. How do…
Urban morphogenesis is the process of formation of its elements and the specialization of its suburbs. Street networks are the structural part of the system. Understand their formation reveals crucial information about urban transformation…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
We perform an analytical investigation of the cell interface dynamics in the framework of a minimal phase field model of cell motility suggested in [1], which consists of two coupled evolution equations for the order parameter and a…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. Computational models can help to integrate available knowledge and to better understand the underlying regulatory logic. We are currently…