Cost and Capacity of Signaling in the Escherichia coli Protein Reaction Network

In systems biology new ways are required to analyze the large amount of existing data on regulation of cellular processes. Recent work can be roughly classified into either dynamical models of well-described subsystems, or coarse-grained descriptions of the topology of the molecular networks at the scale of the whole organism. In order to bridge these two disparate approaches one needs to develop simplified descriptions of dynamics and topological measures which address the propagation of signals in molecular networks. Here, we consider the directed network of protein regulation in E. coli, characterizing its modularity in terms of its potential to transmit signals. We demonstrate that the simplest measure based on identifying sub-networks of strong components, within which each node could send a signal to every other node, indeed partitions the network into functional modules. We then suggest measures to quantify the cost and spread associated with sending a signal between any particular pair of proteins. Thereby, we address the signalling specificity within and between modules, and show that in the regulation of E.coli there is a systematic reduction of the cost and spread for signals traveling over more than two intermediate reactions.Comment: 21 pages, 6 figure

Effect of spatial bias on the nonequilibrium phase transition in a system of coagulating and fragmenting particles

We examine the effect of spatial bias on a nonequilibrium system in which masses on a lattice evolve through the elementary moves of diffusion, coagulation and fragmentation. When there is no preferred directionality in the motion of the masses, the model is known to exhibit a nonequilibrium phase transition between two different types of steady states, in all dimensions. We show analytically that introducing a preferred direction in the motion of the masses inhibits the occurrence of the phase transition in one dimension, in the thermodynamic limit. A finite size system, however, continues to show a signature of the original transition, and we characterize the finite size scaling implications of this. Our analysis is supported by numerical simulations. In two dimensions, bias is shown to be irrelevant.Comment: 7 pages, 7 figures, revte