Functional models for large-scale gene regulation networks: realism and fiction

High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different conditions, times, environments. We now possess a certain amount of information about these two levels of description, stored in libraries, databases and ontologies. A current challenge is to bridge the gap between topology and function, i.e. developing quantitative models aimed at characterizing the expression patterns of large sets of genes. However, approaches that work well for small networks become impossible to master at large scales, mainly because parameters proliferate. In this review we discuss the state of the art of large-scale functional network models, addressing the issue of what can be considered as realistic and what the main limitations may be. We also show some directions for future work, trying to set the goals that future models should try to achieve. Finally, we will emphasize the possible benefits in the understanding of biological mechanisms underlying complex multifactorial diseases, and in the development of novel strategies for the description and the treatment of such pathologies.Comment: to appear on Mol. BioSyst. 200

A new coupling solution for G3-PLC employment in MV smart grids

This paper proposes a new coupling solution for transmitting narrowband multicarrier power line communication (PLC) signals over medium voltage (MV) power lines. The proposed system is based on an innovative PLC coupling principle, patented by the authors, which exploits the capacitive divider embedded in voltage detecting systems (VDS) already installed inside the MV switchboard. Thus, no dedicated couplers have to be installed and no switchboard modifications or energy interruptions are needed. This allows a significant cost reduction of MV PLC implementation. A first prototype of the proposed coupling system was presented in previous papers: it had a 15 kHz bandwidth useful to couple single carrier PSK modulated PLC signals with a center frequency from 50–200 kHz. In this paper, a new prototype is developed with a larger bandwidth, up to 164 kHz, thus allowing to couple multicarrier G3-PLC signals using orthogonal frequency division multiplexing (OFDM) digital modulation. This modulation ensures a more robust communication even in harsh power line channels. In the paper, the new coupling system design is described in detail. A new procedure is presented for tuning the coupling system parameters at first installation in a generic MV switchboard. Finally, laboratory and in-field experimental test results are reported and discussed. The coupling performances are evaluated measuring the throughput and success rate in the case of both 18 and 36 subcarriers, in one of the different tone masks standardized for the FCC-above CENELEC band (that is, from 154.6875–487.5 kHz). The experimental results show an efficient behavior of the proposed coupler allowing a two-way communication of G3-PLC OFDM signals on MV networks

Fixed points of dynamic processes of set-valued F-contractions and application to functional equations

The article is a continuation of the investigations concerning F-contractions which have been recently introduced in [Wardowski in Fixed Point Theory Appl. 2012:94,2012]. The authors extend the concept of F-contractive mappings to the case of nonlinear F-contractions and prove a fixed point theorem via the dynamic processes. The paper includes a non-trivial example which shows the motivation for such investigations. The work is summarized by the application of the introduced nonlinear F-contractions to functional equations

Universal Features in the Genome-level Evolution of Protein Domains

Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are probabilities of duplication, innovation, and loss of domains. However, no one so far has addressed the issue that these distributions follow definite trends depending on protein-coding genome size only. We present a stochastic duplication/innovation model, falling in the class of so-called Chinese Restaurant Processes, able to explain this feature of the data. Using only two universal parameters, related to a minimal number of domains and to the relative weight of innovation to duplication, the model reproduces two important aspects: (a) the populations of domain classes (the sets, related to homology classes, containing realizations of the same domain in different proteins) follow common power-laws whose cutoff is dictated by genome size, and (b) the number of domain families is universal and markedly sublinear in genome size. An important ingredient of the model is that the innovation probability decreases with genome size. We propose the possibility to interpret this as a global constraint given by the cost of expanding an increasingly complex interactome. Finally, we introduce a variant of the model where the choice of a new domain relates to its occurrence in genomic data, and thus accounts for fold specificity. Both models have general quantitative agreement with data from hundreds of genomes, which indicates the coexistence of the well-known specificity of proteomes with robust self-organizing phenomena related to the basic evolutionary ``moves'' of duplication and innovation

Fluctuations of a driven membrane in an electrolyte

We develop a model for a driven cell- or artificial membrane in an electrolyte. The system is kept far from equilibrium by the application of a DC electric field or by concentration gradients, which causes ions to flow through specific ion-conducting units (representing pumps, channels or natural pores). We consider the case of planar geometry and Debye-H\"{u}ckel regime, and obtain the membrane equation of motion within Stokes hydrodynamics. At steady state, the applied field causes an accumulation of charges close to the membrane, which, similarly to the equilibrium case, can be described with renormalized membrane tension and bending modulus. However, as opposed to the equilibrium situation, we find new terms in the membrane equation of motion, which arise specifically in the out-of-equilibrium case. We show that these terms lead in certain conditions to instabilities.Comment: 7 pages, 2 figures. submitted to Europhys. Let