Uniform sampling of steady states in metabolic networks: heterogeneous scales and rounding

The uniform sampling of convex polytopes is an interesting computational problem with many applications in inference from linear constraints, but the performances of sampling algorithms can be affected by ill-conditioning. This is the case of inferring the feasible steady states in models of metabolic networks, since they can show heterogeneous time scales . In this work we focus on rounding procedures based on building an ellipsoid that closely matches the sampling space, that can be used to define an efficient hit-and-run (HR) Markov Chain Monte Carlo. In this way the uniformity of the sampling of the convex space of interest is rigorously guaranteed, at odds with non markovian methods. We analyze and compare three rounding methods in order to sample the feasible steady states of metabolic networks of three models of growing size up to genomic scale. The first is based on principal component analysis (PCA), the second on linear programming (LP) and finally we employ the lovasz ellipsoid method (LEM). Our results show that a rounding procedure is mandatory for the application of the HR in these inference problem and suggest that a combination of LEM or LP with a subsequent PCA perform the best. We finally compare the distributions of the HR with that of two heuristics based on the Artificially Centered hit-and-run (ACHR), gpSampler and optGpSampler. They show a good agreement with the results of the HR for the small network, while on genome scale models present inconsistencies.Comment: Replacement with major revision

The Interrupted Power Law and The Size of Shadow Banking

Using public data (Forbes Global 2000) we show that the asset sizes for the largest global firms follow a Pareto distribution in an intermediate range, that is ``interrupted'' by a sharp cut-off in its upper tail, where it is totally dominated by financial firms. This flattening of the distribution contrasts with a large body of empirical literature which finds a Pareto distribution for firm sizes both across countries and over time. Pareto distributions are generally traced back to a mechanism of proportional random growth, based on a regime of constant returns to scale. This makes our findings of an ``interrupted'' Pareto distribution all the more puzzling, because we provide evidence that financial firms in our sample should operate in such a regime. We claim that the missing mass from the upper tail of the asset size distribution is a consequence of shadow banking activity and that it provides an (upper) estimate of the size of the shadow banking system. This estimate -- which we propose as a shadow banking index -- compares well with estimates of the Financial Stability Board until 2009, but it shows a sharper rise in shadow banking activity after 2010. Finally, we propose a proportional random growth model that reproduces the observed distribution, thereby providing a quantitative estimate of the intensity of shadow banking activity.Comment: 12 pages, 5 figures, 2 tables. To appear in Plos ONE 201

Reading entanglement in terms of spin configurations in quantum magnets

We consider a quantum many-body system made of $N$ interacting $S{=}1/2$ spins on a lattice, and develop a formalism which allows to extract, out of conventional magnetic observables, the quantum probabilities for any selected spin pair to be in maximally entangled or factorized two-spin states. This result is used in order to capture the meaning of entanglement properties in terms of magnetic behavior. In particular, we consider the concurrence between two spins and show how its expression extracts information on the presence of bipartite entanglement out of the probability distributions relative to specific sets of two-spin quantum states. We apply the above findings to the antiferromagnetic Heisenberg model in a uniform magnetic field, both on a chain and on a two-leg ladder. Using Quantum Monte Carlo simulations, we obtain the above probability distributions and the associated entanglement, discussing their evolution under application of the field.Comment: Final version, to appear in European Physical Journal

Planar master integrals for the two-loop light-fermion electroweak corrections to Higgs plus jet production

We present the analytic calculation of the planar master integrals which contribute to compute the two-loop light-fermion electroweak corrections to the production of a Higgs boson in association with a jet in gluon-gluon fusion. The complete dependence on the electroweak-boson mass is retained. The master integrals are evaluated by means of the differential equations method and the analytic results are expressed in terms of multiple polylogarithms up to weight four.Comment: 21 pages, ancillary file

Impact of urbanization on predator and parasitoid insects at multiple spatial scales

Landscapes are becoming increasingly urbanized, causing loss and fragmentation of natural habitats, with potentially negative effects on biodiversity. Insects are among the organisms with the largest diversity in urbanized environments. Here, we sampled predator (Ampulicidae, Sphecidae and Crabronidae) and parasitoid (Tachinidae) flower-visiting insects in 36 sites in the city of Rome (Italy). Although the diversity of herbivorous insects in urban areas mostly depends on the availability of flowering plants and nesting sites, predators and parasitoids generally require a larger number of resources during their life cycle, and are expected to be particularly influenced by urbanization. As flower-visitors can easily move between habitat patches, the effect of urbanization was tested at multiple spatial scales (local, landscape and sub-regional). We found that urbanization influenced predator and parasitoid flower-visitors at all three spatial scales. At the local scale, streets and buildings negatively influenced evenness of predators and species richness and abundance of parasitoids probably acting as dispersal barrier. At the landscape scale, higher percentage of urban decreased predator abundance, while increasing their evenness, suggesting an increase in generalist and highly mobile species. Area and compactness (i.e. Contiguity index) of urban green interactively influenced predator communities, whereas evenness of parasitoids increased with increasing Contiguity index. At the sub-regional scale, species richness and abundance of predators increased with increasing distance from the city center. Compared to previous studies testing the effect of urbanization, we found little variation in species richness, abundance and evenness along our urbanization gradient. The current insect fauna has been probably selected for its tolerance to habitat loss and fragmentation, being the result of the intensive anthropogenic alteration occurred in the area in the last centuries. Conservation strategies aimed at predator and parasitoid flying insects have to take in account variables at multiple spatial-scales, as well as the complementarity of resources across the landscape

Transforming nonlocality into frequency dependence: a shortcut to spectroscopy

Measurable spectra are theoretically very often derived from complicated many-body Green's functions. In this way, one calculates much more information than actually needed. Here we present an in principle exact approach to construct effective potentials and kernels for the direct calculation of electronic spectra. In particular, the potential that yields the spectral function needed to describe photoemission turns out to be dynamical but {\it local} and {\it real}. As example we illustrate this ``photoemission potential'' for sodium and aluminium, modelled as homogeneous electron gas, and discuss in particular its frequency dependence stemming from the nonlocality of the corresponding self-energy. We also show that our approach leads to a very short derivation of a kernel that is known to well describe absorption and energy-loss spectra of a wide range of materials

Master Integrals for the two-loop, non-planar QCD corrections to top-quark pair production in the quark-annihilation channel

We present the analytic calculation of the Master Integrals for the two-loop, non-planar topologies that enter the calculation of the amplitude for top-quark pair hadroproduction in the quark-annihilation channel. Using the method of differential equations, we expand the integrals in powers of the dimensional regulator $\epsilon$ and determine the expansion coefficients in terms of generalized harmonic polylogarithms of two dimensionless variables through to weight four.Comment: 28 pages, 2 figures, ancillary files include