Related papers: Irreversibility in Bacterial Regulatory Networks
Objective: Brain is a fantastic organ that helps creature adapting to the environment. Network is the most essential structure of brain, but the capability of a simple network is still not very clear. In this study, we try to expound some…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. They also tend to have broad distributions for the out-degree. What mechanisms might be responsible for these…
The relation between network structure and dynamics is determinant for the behavior of complex systems in numerous domains. An important long-standing problem concerns the properties of the networks that optimize the dynamics with respect…
Based on extensive study of a dynamical systems model of the development of a cell society, a novel theory for stem cell differentiation and its regulation is proposed as the ``chaos hypothesis''. Two fundamental features of stem cell…
Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the…
This article traces the development of fluctuation theory and its deep connection to irreversibility, from equilibrium to near-equilibrium, and finally to far-from-equilibrium systems. Classical fluctuation theorems, which capture the…
In a recent paper, it has been suggested that the controllability of a diffusively coupled complex network, subject to localized feedback loops at some of its vertices, can be assessed by means of a Master Stability Function approach, where…
It is generally recognized that a distinguishing feature of life is its peculiar capability to avoid equilibration. The origin of this capability and its evolution along the timeline of abiogenesis is not yet understood. We propose to study…
One of the well-known results in concurrency theory concerns the relationship between event structures and occurrence nets: an occurrence net can be associated with a prime event structure, and vice versa. More generally, the relationships…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…
Irreversible aggregation is revisited in view of recent work on renormalization of complex networks. Its scaling laws and phase transitions are related to percolation transitions seen in the latter. We illustrate our points by giving the…
Many social, technological and biological interactions involve network relationships whose outcome intimately depends on the structure of the network and on the strengths of the connections. Yet, although much information is now available…
We evaluate the probability that a Boolean network returns to an attractor after perturbing h nodes. We find that the return probability as function of h can display a variety of different behaviours, which yields insights into the…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
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…
Traditional percolation theory assumes static microscopic rules, limiting its ability to describe real-world complex systems where macroscopic order actively regulates local interactions. Here, we introduce feedback percolation, an unified…
Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts such as development and mutation, but not for acquiring new functions (i.e. emergence). Here, we…
Bacterial chemotaxis in Escherichia coli is a canonical system for the study of signal transduction. A remarkable feature of this system is the coexistence of precise adaptation in population with large fluctuating cellular behavior in…
Social ecological systems are often difficult to investigate and manage because of their inherent complexity1. Small variations in external drivers can lead to abrupt changes associated with instabilities and bifurcations in the underlying…
Understanding and predicting the evolution of across complex systems remains a fundamental challenge due to the absence of unified and computationally testable frameworks. Here we propose the Recursive Hierarchical Network(RHN),…