Protein Evolution in Yeast Transcription Factor Subnetworks

When averaged over the full yeast protein–protein interaction and transcriptional regulatory networks, protein hubs with many interaction partners or regulators tend to evolve significantly more slowly due to increased negative selection. However, genome-wide analysis of protein evolution in the subnetworks of associations involving yeast transcription factors (TFs) reveals that TF hubs do not tend to evolve significantly more slowly than TF non-hubs. This result holds for all four major types of TF hubs: interaction hubs, regulatory in-degree and out-degree hubs, as well as co-regulatory hubs that jointly regulate target genes with many TFs. Furthermore, TF regulatory in-degree hubs tend to evolve significantly more quickly than TF non-hubs. Most importantly, the correlations between evolutionary rate (KA/KS) and degrees for TFs are significantly more positive than those for generic proteins within the same global protein–protein interaction and transcriptional regulatory networks. Compared to generic protein hubs, TF hubs operate at a higher level in the hierarchical structure of cellular networks, and hence experience additional evolutionary forces (relaxed negative selection or positive selection through network rewiring). The striking difference between the evolution of TF hubs and generic protein hubs demonstrates that components within the same global network can be governed by distinct organizational and evolutionary principles.National Natural Science Foundation of China (10801131, 10631070); National Science Foundation (DGE-0654108); Pharmaceutical Research and Manufacturers of America Foundation (Research Starter Grant in Informatics); K. C. Wong Education Foundatio

Remote Preparation of Mixed States via Noisy Entanglement

We present a practical and general scheme of remote preparation for pure and mixed state, in which an auxiliary qubit and controlled-NOT gate are used. We discuss the remote state preparation (RSP) in two important types of decoherent channel (depolarizing and dephaseing). In our experiment, we realize RSP in the dephaseing channel by using spontaneous parametric down conversion (SPDC), linear optical elements and single photon detector.Comment: 10 pages, 5 figures, submitted to PR

Congestion-gradient driven transport on complex networks

We present a study of transport on complex networks with routing based on local information. Particles hop from one node of the network to another according to a set of routing rules with different degrees of congestion awareness, ranging from random diffusion to rigid congestion-gradient driven flow. Each node can be either source or destination for particles and all nodes have the same routing capacity, which are features of ad-hoc wireless networks. It is shown that the transport capacity increases when a small amount of congestion awareness is present in the routing rules, and that it then decreases as the routing rules become too rigid when the flow becomes strictly congestion-gradient driven. Therefore, an optimum value of the congestion awareness exists in the routing rules. It is also shown that, in the limit of a large number of nodes, networks using routing based on local information jam at any nonzero load. Finally, we study the correlation between congestion at node level and a betweenness centrality measure.Comment: 11 pages, 8 figure

Optimal routing on complex networks

We present a novel heuristic algorithm for routing optimization on complex networks. Previously proposed routing optimization algorithms aim at avoiding or reducing link overload. Our algorithm balances traffic on a network by minimizing the maximum node betweenness with as little path lengthening as possible, thus being useful in cases when networks are jamming due to queuing overload. By using the resulting routing table, a network can sustain significantly higher traffic without jamming than in the case of traditional shortest path routing.Comment: 4 pages, 5 figure

Quantum Hall effect on centimeter scale chemical vapor deposited graphene films

We report observations of well developed half integer quantum Hall effect (QHE) on mono layer graphene films of 7 mm \times 7 mm in size. The graphene films are grown by chemical vapor deposition (CVD) on copper, then transferred to SiO_{2} /Si substrates, with typical carrier mobilities \approx 4000 cm^{2} /Vs. The large size graphene with excellent quality and electronic homogeneity demonstrated in this work is promising for graphene-based quantum Hall resistance standards, and can also facilitate a wide range of experiments on quantum Hall physics of graphene and practical applications exploiting the exceptional properties of graphene

Transport optimization on complex networks

We present a comparative study of the application of a recently introduced heuristic algorithm to the optimization of transport on three major types of complex networks. The algorithm balances network traffic iteratively by minimizing the maximum node betweenness with as little path lengthening as possible. We show that by using this optimal routing, a network can sustain significantly higher traffic without jamming than in the case of shortest path routing. A formula is proved that allows quick computation of the average number of hops along the path and of the average travel times once the betweennesses of the nodes are computed. Using this formula, we show that routing optimization preserves the small-world character exhibited by networks under shortest path routing, and that it significantly reduces the average travel time on congested networks with only a negligible increase in the average travel time at low loads. Finally, we study the correlation between the weights of the links in the case of optimal routing and the betweennesses of the nodes connected by them.Comment: 19 pages, 7 figure