A statistical mechanics description of environmental variability in metabolic networks

Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks display considerable asymmetry. In this paper, we explore possible evolutionary factors pertaining to the reduced symmetry observed in these networks, and demonstrate the important role environmental variability plays in shaping their structural organization. Interpreting the returnability index as an equilibrium constant for a reaction network in equilibrium with a hypothetical reference system, enables us to quantify the extent to which a metabolic network is in disequilibrium. Further, by introducing a new directed centrality measure via an extension of the subgraph centrality metric to directed networks, we are able to characterise individual metabolites by their participation within metabolic pathways. To demonstrate these ideas, we study 116 metabolic networks of bacteria. In particular, we find that the equilibrium constant for the metabolic networks decreases significantly in-line with variability in bacterial habitats, supporting the view that environmental variability promotes disequilibrium within these biochemical reaction system

Statistically derived contributions of diverse human influences to twentieth-century temperature changes

The warming of the climate system is unequivocal as evidenced by an increase in global temperatures by 0.8 °C over the past century. However, the attribution of the observed warming to human activities remains less clear, particularly because of the apparent slow-down in warming since the late 1990s. Here we analyse radiative forcing and temperature time series with state-of-the-art statistical methods to address this question without climate model simulations. We show that long-term trends in total radiative forcing and temperatures have largely been determined by atmospheric greenhouse gas concentrations, and modulated by other radiative factors. We identify a pronounced increase in the growth rates of both temperatures and radiative forcing around 1960, which marks the onset of sustained global warming. Our analyses also reveal a contribution of human interventions to two periods when global warming slowed down. Our statistical analysis suggests that the reduction in the emissions of ozone-depleting substances under the Montreal Protocol, as well as a reduction in methane emissions, contributed to the lower rate of warming since the 1990s. Furthermore, we identify a contribution from the two world wars and the Great Depression to the documented cooling in the mid-twentieth century, through lower carbon dioxide emissions. We conclude that reductions in greenhouse gas emissions are effective in slowing the rate of warming in the short term.F.E. acknowledges financial support from the Consejo Nacional de Ciencia y Tecnologia (http://www.conacyt.gob.mx) under grant CONACYT-310026, as well as from PASPA DGAPA of the Universidad Nacional Autonoma de Mexico. (CONACYT-310026 - Consejo Nacional de Ciencia y Tecnologia; PASPA DGAPA of the Universidad Nacional Autonoma de Mexico

Dynamic communicability predicts infectiousness

Using real, time-dependent social interaction data, we look at correlations between some recently proposed dynamic centrality measures and summaries from large-scale epidemic simulations. The evolving network arises from email exchanges. The centrality measures, which are relatively inexpensive to compute, assign rankings to individual nodes based on their ability to broadcast information over the dynamic topology. We compare these with node rankings based on infectiousness that arise when a full stochastic SI simulation is performed over the dynamic network. More precisely, we look at the proportion of the network that a node is able to infect over a fixed time period, and the length of time that it takes for a node to infect half the network.We find that the dynamic centrality measures are an excellent, and inexpensive, proxy for the full simulation-based measures

Resistance distance, information centrality, node vulnerability and vibrations in complex networks

We discuss three seemingly unrelated quantities that have been introduced in different fields of science for complex networks. The three quantities are the resistance distance, the information centrality and the node displacement. We first prove various relations among them. Then we focus on the node displacement, showing its usefulness as an index of node vulnerability.We argue that the node displacement has a better resolution as a measure of node vulnerability than the degree and the information centrality

Distribution of shortest cycle lengths in random networks

We present analytical results for the distribution of shortest cycle lengths (DSCL) in random networks. The approach is based on the relation between the DSCL and the distribution of shortest path lengths (DSPL). We apply this approach to configuration model networks, for which analytical results for the DSPL were obtained before. We first calculate the fraction of nodes in the network which reside on at least one cycle. Conditioning on being on a cycle, we provide the DSCL over ensembles of configuration model networks with degree distributions which follow a Poisson distribution (Erdos-R\'enyi network), degenerate distribution (random regular graph) and a power-law distribution (scale-free network). The mean and variance of the DSCL are calculated. The analytical results are found to be in very good agreement with the results of computer simulations.Comment: 44 pages, 11 figure

Correlation, Network and Multifractal Analysis of Global Financial Indices

We apply RMT, Network and MF-DFA methods to investigate correlation, network and multifractal properties of 20 global financial indices. We compare results before and during the financial crisis of 2008 respectively. We find that the network method gives more useful information about the formation of clusters as compared to results obtained from eigenvectors corresponding to second largest eigenvalue and these sectors are formed on the basis of geographical location of indices. At threshold 0.6, indices corresponding to Americas, Europe and Asia/Pacific disconnect and form different clusters before the crisis but during the crisis, indices corresponding to Americas and Europe are combined together to form a cluster while the Asia/Pacific indices forms another cluster. By further increasing the value of threshold to 0.9, European countries France, Germany and UK constitute the most tightly linked markets. We study multifractal properties of global financial indices and find that financial indices corresponding to Americas and Europe almost lie in the same range of degree of multifractality as compared to other indices. India, South Korea, Hong Kong are found to be near the degree of multifractality of indices corresponding to Americas and Europe. A large variation in the degree of multifractality in Egypt, Indonesia, Malaysia, Taiwan and Singapore may be a reason that when we increase the threshold in financial network these countries first start getting disconnected at low threshold from the correlation network of financial indices. We fit Binomial Multifractal Model (BMFM) to these financial markets.Comment: 32 pages, 25 figures, 1 tabl

The BES f_0(1810): a new glueball candidate

We analyze the f_0(1810) state recently observed by the BES collaboration via radiative J/\psi decay to a resonant \phi\omega spectrum and confront it with DM2 data and glueball theory. The DM2 group only measured \omega\omega decays and reported a pseudoscalar but no scalar resonance in this mass region. A rescattering mechanism from the open flavored KKbar decay channel is considered to explain why the resonance is only seen in the flavor asymmetric \omega\phi branch along with a discussion of positive C parity charmonia decays to strengthen the case for preferred open flavor glueball decays. We also calculate the total glueball decay width to be roughly 100 MeV, in agreement with the narrow, newly found f_0, and smaller than the expected estimate of 200-400 MeV. We conclude that this discovered scalar hadron is a solid glueball candidate and deserves further experimental investigation, especially in the K-Kbar channel. Finally we comment on other, but less likely, possible assignments for this state.Comment: 11 pages, 4 figures. Major substantive additions, including an ab-initio, QCD-based computation of the glueball inclusive decay width, evaluation of final state effects, and enhanced discussion of several alternative possibilities. Our conclusions are unchanged: the BES f_0(1810) is a promising glueball candidat

Googling the brain: discovering hierarchical and asymmetric network structures, with applications in neuroscience

Hierarchical organisation is a common feature of many directed networks arising in nature and technology. For example, a well-defined message-passing framework based on managerial status typically exists in a business organisation. However, in many real-world networks such patterns of hierarchy are unlikely to be quite so transparent. Due to the nature in which empirical data is collated the nodes will often be ordered so as to obscure any underlying structure. In addition, the possibility of even a small number of links violating any overall “chain of command” makes the determination of such structures extremely challenging. Here we address the issue of how to reorder a directed network in order to reveal this type of hierarchy. In doing so we also look at the task of quantifying the level of hierarchy, given a particular node ordering. We look at a variety of approaches. Using ideas from the graph Laplacian literature, we show that a relevant discrete optimization problem leads to a natural hierarchical node ranking. We also show that this ranking arises via a maximum likelihood problem associated with a new range-dependent hierarchical random graph model. This random graph insight allows us to compute a likelihood ratio that quantifies the overall tendency for a given network to be hierarchical. We also develop a generalization of this node ordering algorithm based on the combinatorics of directed walks. In passing, we note that Google’s PageRank algorithm tackles a closely related problem, and may also be motivated from a combinatoric, walk-counting viewpoint. We illustrate the performance of the resulting algorithms on synthetic network data, and on a real-world network from neuroscience where results may be validated biologically