arXiv subjects

Enrico Borriello

Publications and source records attributed to Enrico Borriello.

16 recordsLinked to original sources

arXiv2024

Difficult control is related to instability in biologically inspired Boolean networks

Previous work in Boolean dynamical networks has suggested that the number of components that must be controlled to select an existing attractor is typically set by the number of attractors admitted by the dynamics, with no dependence on the size of the network. Here we study the rare cases of networks that defy this expectation, with attractors that require controlling most nodes. We find empirically that unstable fixed points are the primary recurring characteristic of networks that prove more difficult to control. We describe an efficient way to identify unstable fixed points and show that, in both existing biological models and ensembles of random dynamics, we can better explain the variance of control kernel sizes by incorporating the prevalence of unstable fixed points. In the end, the association of these outliers with dynamics that are unstable to small perturbations reveals them as artifacts of deterministic models, making them less biologically relevant and reinforcing the generality of easy controllability in biological networks.

q-bio.MN↗

arXiv2024

Diagrammatic Rules for Triad Census

In network theory, a triad census is a method designed to categorize and enumerate the various types of subgraphs with three nodes and their connecting edges within a network. Triads serve as fundamental building blocks for comprehending the structure and dynamics of networks, and the triad census offers a systematic approach to their classification. Typically, triad counts are obtained numerically, but lesser-known methods have been developed to precisely evaluate them without the need for sampling. In our study, we build upon Moody's matrix approach, presenting general diagrammatic rules that systematically and intuitively generate closed formulas for the occurrence numbers of triads in a network.

physics.soc-ph↗

arXiv2021

The basis of easy controllability in Boolean networks

Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the effectiveness of external control in selecting a desired final state when that state is among the original attractors of the dynamics. Analyzing 49 existing biological network models, we find strong numerical evidence that the average number of nodes that must be forced scales logarithmically with the number of original attractors. This suggests that biological networks may be typically easy to control even when the number of interacting components is large. We provide a theoretical explanation of the scaling by separating controlling nodes into three types: those that act as inputs, those that distinguish among attractors, and any remaining nodes. We further identify characteristics of dynamics that can invalidate this scaling, and speculate about how this relates more broadly to non-biological systems.

q-bio.MN↗

arXiv2021

Evolution of default genetic control mechanisms

We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state of the cell as well as the environment to control expression of a coding region. Control and coding regions evolve to maximize a fitness function between expressed coding sequences and the environment. 118 runs of the model run to an average of 1.4 x 10^6 `generations' each with a range of starting parameters probed the conditions under which genomes evolved a `default style' of control. Unexpectedly, the control logic that evolved was not significantly correlated to the complexity of the environment. Genetic logic was strongly correlated with genome complexity and with the fraction of genes active in the cell at any one time. More complex genomes correlated with the evolution of genetic controls in which genes were active (`default on'), and a low fraction of genes being expressed correlated with a genetic logic in which genes were biased to being inactive unless positively activated (`default off' logic). We discuss how this might relate to the evolution of the complex eukaryotic genome, which operates in a `default off' mode.

q-bio.GN↗

arXiv2019

A unified formal framework for developmental andevolutionary change in gene regulatory network models

The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell states controlled by hierarchies of regulatory structures. It occurs over the lifetime of a single individual, and is associated to the gene expression level change of a given genotype. Evolution, by contrast entails genotypic change through the acquisition/loss of genes and changes in the network topology of interactions among genes. It involves the emergence of new, environmentally selected phenotypes over the lifetimes of many individuals. Here we present a model of regulatory network evolution that accounts for both timescales. We extend the framework of Boolean models of gene regulatory networks (GRN)-currently only applicable to describing development to include evolutionary processes. As opposed to one-to-one maps to specific attractors, we identify the phenotypes of the cells as the relevant macrostates of the GRN. A phenotype may now correspond to multiple attractors, and its formal definition no longer requires a fixed size for the genotype. This opens the possibility for a quantitative study of the phenotypic change of a genotype, which is itself changing over evolutionary timescales. We show how the realization of specific phenotypes can be controlled by gene duplication events (used here as an archetypal evolutionary event able to change the genotype), and how successive events of gene duplication lead to new regulatory structures via selection. At the same time, we show that our generalized framework does not inhibit network controllability and the possibility for network control theory to describe epigenetic signaling during development.

physics.bio-ph↗

arXiv2017

An information-based classification of Elementary Cellular Automata

A novel, information-based classification of elementary cellular automata is proposed that circumvents the problems associated with isolating whether complexity is in fact intrinsic to a dynamical rule, or if it arises merely as a product of a complex initial state. Transfer entropy variations processed by the system split the 256 elementary rules into three information classes, based on sensitivity to initial conditions. These classes form a hierarchy such that coarse-graining transitions observed among elementary cellular automata rules predominately occur within each information- based class, or much more rarely, down the hierarchy.

cs.CC↗

arXiv2014

Turbulence patterns and neutrino flavor transitions in high-resolution supernova models

During the shock-wave propagation in a core-collapse supernova (SN), matter turbulence may affect neutrino flavor conversion probabilities. Such effects have been usually studied by adding parametrized small-scale random fluctuations (with arbitrary amplitude) on top of coarse, spherically symmetric matter density profiles. Recently, however, two-dimensional (2D) SN models have reached a space resolution high enough to directly trace anisotropic density profiles, down to scales smaller than the typical neutrino oscillation length. In this context, we analyze the statistical properties of a large set of SN matter density profiles obtained in a high-resolution 2D simulation, focusing on a post-bounce time (2 s) suited to study shock-wave effects on neutrino propagation on scales as small as O(100) km and possibly below. We clearly find the imprint of a broken (Kolmogorov-Kraichnan) power-law structure, as generically expected in 2D turbulence spectra. We then compute the flavor evolution of SN neutrinos along representative realizations of the turbulent matter density profiles, and observe no or modest damping of the neutrino crossing probabilities on their way through the shock wave. In order to check the effect of possibly unresolved fluctuations at scales below O(100) km, we also apply a randomization procedure anchored to the power spectrum calculated from the simulation, and find consistent results within \pm 1 sigma fluctuations. These results show the importance of anchoring turbulence effects on SN neutrinos to realistic, fine-grained SN models.

astro-ph.SR↗

arXiv2013

Stringent constraint on neutrino Lorentz-invariance violation from the two IceCube PeV neutrinos

It has been speculated that Lorentz-invariance violation (LIV) might be generated by quantum-gravity (QG) effects. As a consequence, particles may not travel at the universal speed of light. In particular, superluminal extragalactic neutrinos would rapidly lose energy via the bremssthralung of electron-positron pairs (nu -> nu e+ e-), damping their initial energy into electromagnetic cascades, a figure constrained by Fermi-LAT data. We show that the two cascade neutrino events with energies around 1 PeV recently detected by IceCube -if attributed to extragalactic diffuse events, as it appears likely- can place the strongest bound on LIV in the neutrino sector, namely delta =(v^2-1) < O(10^(-18)), corresponding to a QG scale M_QG ~ 10^5 M_Pl (M_QG >~ 10^(-4) M_Pl) for a linear (quadratic) LIV, at least for models inducing superluminal neutrino effects (delta > 0).

astro-ph.HE↗

arXiv2013

The strongest bounds on active-sterile neutrino mixing after Planck data

Light sterile neutrinos can be excited by oscillations with active neutrinos in the early universe. Their properties can be constrained by their contribution as extra-radiation, parameterized in terms of the effective number of neutrino species N_ eff, and to the universe energy density today Ω_νh^2. Both these parameters have been measured to quite a good precision by the Planck satellite experiment. We use this result to update the bounds on the parameter space of (3+1) sterile neutrino scenarios, with an active-sterile neutrino mass squared splitting in the range (10^{-5} - 10^2 ) eV^2. We consider both normal and inverted mass orderings for the active and sterile states. For the first time we take into account the possibility of two non-vanishing active-sterile mixing angles. We find that the bounds are more stringent than those obtained in laboratory experiments. This leads to a strong tension with the short-baseline hints of light sterile neutrinos. In order to relieve this disagreement, modifications of the standard cosmological scenario, e.g. large primordial neutrino asymmetries, are required.

astro-ph.CO↗

arXiv2012

(Down-to-)Earth matter effect in supernova neutrinos

Neutrino oscillations in the Earth matter may introduce peculiar modulations in the supernova (SN) neutrino spectra. The detection of this effect has been proposed as diagnostic tool for the neutrino mass hierarchy at "large" 1-3 leptonic mixing angle theta13. We perform an updated study on the observability of this effect at large next-generation underground detectors (i.e., 0.4 Mton water Cherenkov, 50 kton scintillation and 100 kton liquid Argon detectors) based on neutrino fluxes from state-of-the-art SN simulations and accounting for statistical fluctuations via Montecarlo simulations. Since the average energies predicted by recent simulations are lower than previously expected and a tendency towards the equalization of the neutrino fluxes appears during the SN cooling phase, the detection of the Earth matter effect will be more challenging than expected from previous studies. We find that none of the proposed detectors shall be able to detect the Earth modulation for the neutrino signal of a typical galactic SN at 10 kpc. It should be observable in a 100 kton liquid Argon detector for a SN at few kpc and all three detectors would clearly see the Earth signature for very close-by stars only (d ~ 0.2 kpc). Finally, we show that adopting IceCube as co-detector together with a Mton water Cherenkov detector is not a viable option either.

hep-ph↗

arXiv2012

Constraints on sterile neutrino dark matter from XMM--Newton observation of M33

Using archival XMM-Newton observations of the diffuse and unresolved components emission in the inner disc of M33 we exclude the possible contribution from narrow line emission in the energy range 0.5-5 keV more intense than 10^{-6}-10^{-5} erg/s. Under the hypothesis that sterile neutrinos constitute the majority of the dark matter in M33, we use this result in order to put constraints on their parameter space in the 1-10 keV mass range.

astro-ph.GA↗

arXiv2011

Dark matter electron anisotropy: a universal upper limit

We study the dipole anisotropy in the arrival directions of high energy CR electrons and positrons (CRE) of Dark Matter (DM) origin. We show that this quantity is very weakly model dependent and offers a viable criterion to discriminate among CRE from DM or from local discrete sources, like e.g. pulsars. In particular, we find that the maximum anisotropy which DM can provide is to a very good approximation a universal quantity and, as a consequence, if a larger anisotropy is detected, this would constitute a strong evidence for the presence of astrophysical local discrete CRE sources, whose anisotropy, instead, can be naturally larger than the DM upper limit. We further find that the main source of anisotropy from DM is given by the fluctuation in the number density of DM sub-structures in the vicinity of the observer and we thus devote special attention to the study of the variance in the sub-structures realization implementing a dedicated Montecarlo simulation. Such scenarios will be probed in the next years by Fermi-LAT, providing new hints, or constraints, about the nature of DM.

astro-ph.HE↗

arXiv2010

Radio emission from dark matter annihilation in the Large Magellanic Cloud

The Large Magellanic Cloud, at only 50 kpc away from us and known to be dark matter dominated, is clearly an interesting place where to search for dark matter annihilation signals. In this paper, we estimate the synchrotron emission due to WIMP annihilation in the halo of the LMC at two radio frequencies, 1.4 and 4.8 GHz, and compare it to the observed emission, in order to impose constraints in the WIMP mass vs. annihilation cross section plane. We use available Faraday rotation data from background sources to estimate the magnitude of the magnetic field in different regions of the LMC's disc, where we calculate the radio signal due to dark matter annihilation. We account for the e+ e- energy losses due to synchrotron, Inverse Compton Scattering and bremsstrahlung, using the observed hydrogen and dust temperature distribution on the LMC to estimate their efficiency. The extensive use of observations, allied with conservative choices adopted in all the steps of the calculation, allow us to obtain very realistic constraints.

astro-ph.HE↗

arXiv2009

Searching for Dark Matter in Messier 33

Among various approaches for indirect detection of dark matter, synchrotron emission due to secondary electrons/positrons produced in galactic WIMPs annihilation is raising an increasing interest. In this paper we propose a new method to derive bounds in the mchi - plane by using radio continuum observations of Messier 33, paying particular attention to a low emitting Radio Cavity. The comparison of the expected radio emission due to the galactic dark matter distribution with the observed one provides bounds which are comparable to those obtained from a similar analysis of the Milky Way. Remarkably, the present results are simply based on archival data and thus largely improvable by means of specifically tailored observations. The potentiality of the method compared with more standard searches is discussed by considering the optimistic situation of a vanishing flux (within the experimental sensitivity) measured inside the cavity by a high resolution radio telescope like ALMA. Under the best conditions our technique is able to produce bounds which are comparable to the ones expected after five years of Fermi LAT data taking for an hadronic annihilation channel. Furthermore, it allows to test the hypothesis that space telescopes like Pamela and Fermi LAT are actually observing electrons and positrons due to galactic dark matter annihilation into leptons.

astro-ph.HE↗

arXiv2009

Radio constraints on dark matter annihilation in the galactic halo and its substructures

Annihilation of Dark Matter usually produces together with gamma rays comparable amounts of electrons and positrons. The e+e- gyrating in the galactic magnetic field then produce secondary synchrotron radiation which thus provides an indirect mean to constrain the DM signal itself. To this purpose, we calculate the radio emission from the galactic halo as well as from its expected substructures and we then compare it with the measured diffuse radio background. We employ a multi-frequency approach using data in the relevant frequency range 100 MHz-100 GHz, as well as the WMAP Haze data at 23 GHz. The derived constraints are of the order =10^{-24} cm3 s^{-1} for a DM mass m_chi=100 GeV sensibly depending however on the astrophysical uncertainties, in particular on the assumption on the galactic magnetic field model. The signal from single bright clumps is instead largely attenuated by diffusion effects and offers only poor detection perspectives.

astro-ph↗

arXiv2008

Radio Signal by Galactic Dark Matter

An interesting strategy for indirect detection of Dark Matter comes through the amounts of electrons and positrons usually emitted by DM pair annihilation. The e+e- gyrating in the galactic magnetic field then produce secondary synchrotron radiation. The radio emission from the galactic halo as well as from its expected substructures if compared with the measured diffuse radio background can provide constraints on the physics of WIMPs. In particular one gets the bound of = 10^{-24} cm^3 s^{-1} for a DM mass m_chi = 100 GeV even though sensibly depending on the astrophysical uncertainties.

astro-ph↗