Learn More
Many signaling systems show adaptation-the ability to reset themselves after responding to a stimulus. We computationally searched all possible three-node enzyme network topologies to identify those that could perform adaptation. Only two major core topologies emerge as robust solutions: a negative feedback loop with a buffering node and an incoherent(More)
Disruption of protein folding in the endoplasmic reticulum (ER) causes unfolded proteins to accumulate, triggering the unfolded protein response (UPR). UPR outputs in turn decrease ER unfolded proteins to close a negative feedback loop. However, because it is infeasible to directly measure the concentration of unfolded proteins in vivo, cells are(More)
Using each node's degree as a proxy for its importance, the topological hierarchy of a complex network is introduced and quantified. We propose a simple dynamical process used to construct networks which are either maximally or minimally hierarchical. Comparison with these extremal cases as well as with random scale-free networks allows us to better(More)
Many toxin-antitoxin (TA) loci are known to strongly repress their own transcription. This auto-inhibition is often called 'conditional cooperativity' as it relies on cooperative binding of TA complexes to operator DNA that occurs only when toxins are in a proper stoichiometric relationship with antitoxins. There has recently been an explosion of interest(More)
BACKGROUND Waves propagating in "excitable media" is a reliable way to transmit signals in space. A fascinating example where living cells comprise such a medium is Dictyostelium D. which propagates waves of chemoattractant to attract distant cells. While neutrophils chemotax in a similar fashion as Dictyostelium D., it is unclear if chemoattractant waves(More)
We study Nowak and May's spatial prisoners' dilemma game driven by mutations (random choices of suboptimal strategies) on empirical social networks. The time evolution of the cooperation level is highly complex containing spikes and steps between quasistable levels. A statistical characterization of the quasistable states and a study of the mechanisms(More)
Signaling pathways and networks determine the ability to communicate in systems ranging from living cells to human society. We investigate how the network structure constrains communication in social-, man-made and biological networks. We find that human networks of governance and collaboration are predictable on teat-a-teat level, reflecting well defined(More)
Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual dependencies. The minimum requirements to maintain a large species diversity on long time scales are in general unknown. Using lichen communities as an example, we propose a model for the evolution of mutually excluding organisms(More)
We investigate and quantify the interplay between topology and the ability to send specific signals in complex networks. We find that in a majority of investigated real-world networks the ability to communicate is favored by the network topology at small distances, but disfavored at larger distances. We further suggest how the ability to locate specific(More)