Related papers: Irreversibility in Bacterial Regulatory Networks
Recent work in the area of interdependent networks has focused on interactions between two systems of the same type. However, an important and ubiquitous class of systems are those involving monitoring and control, an example of…
Self-organization in natural and engineered systems causes the emergence of ordered spatio-temporal motifs. In presence of diffusive species, Turing theory has been widely used to understand the formation of such patterns on continuous…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
The present article introduces a reference framework for discussing resilience of computational systems. Rather than a property that may or may not be exhibited by a system, resilience is interpreted here as the emerging result of a dynamic…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Aggregated phenomena in social sciences and economics are highly dependent on the way individuals interact. To help understanding the interplay between socio-economic activities and underlying social networks, this paper studies a…
Transitions from reversible to irreversible or fluctuating states above a critical density and shear amplitude have been extensively studied in non-thermal cyclically sheared suspensions and amorphous solids. Here, we propose that the same…
We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…
Percolation, the formation of a macroscopic connected component, is a key feature in the description of complex networks. The dynamical properties of a variety of systems can be understood in terms of percolation, including the robustness…
Models of bacterial growth tend to be `irreversible', allowing for the number of bacteria in a colony to increase but not to decrease. By contrast, models of molecular self-assembly are usually `reversible', allowing for addition and…
The understanding of epidemics on networks has greatly benefited from the recent application of message-passing approaches, which allow to derive exact results for irreversible spreading (i.e. diseases with permanent acquired immunity) in…
We construct and investigate Boolean networks that follow a given reliable trajectory in state space, which is insensitive to fluctuations in the updating schedule, and which is also robust against noise. Robustness is quantified as the…
One of the characteristic features of genetic networks is their inherent robustness, that is, their ability to retain functionality in spite of the introduction of random errors. In this paper, we seek to better understand how robustness is…
Curiously overlooked in physics is its dependence on the transmission of numbers. For example the transmission of numerical clock readings is implicit in the concept of a coordinate system. The transmission of numbers and other logical…
This paper deals with gene networks whose dynamics is assumed to be generated by a continuous-time, linear, time invariant, finite dimensional system (LTI) at steady state. In particular, we deal with the problem of network reconstruction…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…