The Minimal Controllability Problem for structured systems

This paper considers the Minimal Controllability Problem (MCP), {\em i.e.} the problem of controlling a linear system with an input vector having as few non-zero entries as possible. We focus on structured systems which represent an interesting class of parameter dependent linear systems and look for structural controllability properties based on the sparsity pattern of the input vector. We show first that the MCP is solvable when a rank condition is satisfied and show that generically one non-zero entry in the input vector is sufficient to achieve controllability when there is no specific system structure. We give, according to the fixed zero/non-zero pattern of the state matrix entries, the minimum number and the possible location of non-zero entries in the input vector to ensure generic controllability. The analysis based on graph tools provides with a simple polynomial MCP solution and highlights the structural mechanisms that make it useful to act on some variables to ensure controllability

Nodal dynamics, not degree distributions, determine the structural controllability of complex networks

Structural controllability has been proposed as an analytical framework for making predictions regarding the control of complex networks across myriad disciplines in the physical and life sciences (Liu et al., Nature:473(7346):167-173, 2011). Although the integration of control theory and network analysis is important, we argue that the application of the structural controllability framework to most if not all real-world networks leads to the conclusion that a single control input, applied to the power dominating set (PDS), is all that is needed for structural controllability. This result is consistent with the well-known fact that controllability and its dual observability are generic properties of systems. We argue that more important than issues of structural controllability are the questions of whether a system is almost uncontrollable, whether it is almost unobservable, and whether it possesses almost pole-zero cancellations.Comment: 1 Figures, 6 page

Observability in Connected Strongly Regular Graphs and Distance Regular Graphs

International audienceThis paper concerns the study of observability in consensus networks modeled with strongly regular graphs or distance regular graphs. We first give a Kalman-like simple algebraic criterion for observability in distance regular graphs. This criterion consists in evaluating the rank of a matrix built with the components of the Bose-Mesner algebra associated with the considered graph. Then, we define some bipartite graphs that capture the observability properties of the graph to be studied. In particular, we show that necessary and sufficient observability conditions are given by the nullity of the so-called local bipartite observability graph (resp. local unfolded bipartite observability graph) for strongly regular graphs (resp. distance regular graphs). When the nullity cannot be derived directly from the structure of these bipartite graphs, the rank of the associated bi-adjacency matrix allows evaluating observability. Eventually, as a by-product of the main results we show that non-observability can be stated just by comparing the valency of the graph to be studied with a bound computed from the number of vertices of the graph and its diameter. Similarly nonobservability can also be stated by evaluating the size of the maximum matching in the above mentioned bipartite graphs

Engineering microbial fuel cell biofilm communities

Bioelectrochemical systems, such as microbial fuel cells (MFCs), are a specialized branch of biotechnology which aims to use the diversity of microbial metabolism for industrial applications including: the treatment of wastewater coupled with the production of electricity; the production of high value compounds (e.g. hydrogen); and biosensing applications. MFC technologies use exoelectrogenic bacteria such as Geobacter sp. These bacteria possess a particular metabolism that allows them to exchange electrons with solid surfaces like electrodes. One major parameter that can limit efficient electron transfer from biofilms to the electrode is the metabolic capability and microbial composition of the biofilm. Consequently, a main focus of this research was to determine if it is possible to select and maintain stable electrode biofilm communities that have efficient electron transfer properties and are suitable for specific functions such as biological oxygen demand (BOD) biosensing and electricity production. To achieve this objective, the influence of four parameters including the anode potential, the inoculum source, the substrate and the electrode surface properties, was tested on the selection of exoelectrogenic biofilms. The differences in community structures and electrochemical properties of the different biofilms selected were investigated using population profiling (e.g. SSCP, ARISA, RFLP), cloning and electrochemical analysis (e.g. cyclic voltammetry, power curves). Here, I present evidence that these four parameters altered the dominant community of the selected biofilms, with the anode potential and the substrate having the most effects. These results enrich an ongoing controversy in the literature as to whether electrode potential can influence the composition of anode-respiring biofilms or if they physiologically adapt to different potentials. In this study, I proved that the anode potential affects the composition of Geobacter-dominated biofilms at a strain level. My results imply that it is possible to select for high current-producing biofilms using specific anode potentials. In addition to microbial composition, operational stability of anode-respiring biofilm communities is also of importance for electricity production and the development of biosensors. In this study, I explored the use of a biosensor based on an exoelectrogenic biofilm for the real-time monitoring of BOD, as a fast alternative to the conventional 5-day BOD assay. A Geobacter-dominated biofilm was selected at an anode potential of -0.36 V vs Ag/AgCl with ethanol as the sole carbon source. The biofilm had a broad metabolic capability and accurately quantified the BOD of complex media, opening the way to a new generation of biosensors. Although MFCs are mainly limited by the efficiency of electron transfer at the anode, processes such as the reduction of oxygen at the cathode can also alter the current output of these systems. In this work, I demonstrated that photosynthetic cathodic biofilms enhance the power output of microbial fuel cells by saturating the catholyte in oxygen under illumination. This project contributes significant knowledge to the parameters affecting the formation of anode- respiring biofilms, especially those dominated by Geobacter sp., the dynamics of their community structures, their operational stability and their potential use as BOD biosensors. It also provides evidence of the utility of photosynthetic biofilms to overcome cathodic limitations caused by low rates of the oxygen reduction reaction. The combination of my key research findings provides substantial opportunities to enhance the reliable use and implementation of MFC technologies for environmental monitoring and energy production applications

Functional target controllability of networks: structural properties and efficient algorithms

In this paper we consider the problem of controlling a limited number of target nodes of a network. Equivalently, we can see this problem as controlling the target variables of a structured system, where the state variables of the system are associated to the nodes of the network. We deal with this problem from a different point of view as compared to most recent literature. Indeed, instead of considering controllability in the Kalman sense, that is, as the ability to drive the target states to a desired value, we consider the stronger requirement of driving the target variables as time functions. The latter notion is called functional target controllability. We think that restricting the controllability requirement to a limited set of important variables justifies using a more accurate notion of controllability for these variables. Remarkably, the notion of functional controllability allows formulating very simple graphical conditions for target controllability in the spirit of the structural approach to controllability. The functional approach enables us, moreover, to determine the smallest set of steering nodes that need to be actuated to ensure target controllability, where these steering nodes are constrained to belong to a given set. We show that such a smallest set can be found in polynomial time. We are also able to classify the possible actuated variables in terms of their importance with respect to the functional target controllability problem.Comment: 10 pages, 4 diagrams; to appear in the IEEE Transactions on Network Science and Engineerin

Mobilization of a diatom mutator-like element (MULE) transposon inactivates the uridine monophosphate synthase (UMPS) locus in Phaeodactylum tricornutum.

Diatoms are photosynthetic unicellular microalgae that drive global ecological phenomena in the biosphere and are emerging as sustainable feedstock for an increasing number of industrial applications. Diatoms exhibit enormous taxonomic and genetic diversity, which often results in peculiar biochemical and biological traits. Transposable elements (TEs) represent a substantial portion of diatom genomes and have been hypothesized to exert a relevant role in enriching genetic diversity and making a core contribution to genome evolution. Here, through long-read whole-genome sequencing, we identified a mutator-like element (MULE) in the model diatom Phaeodactylum tricornutum, and we report the direct observation of its mobilization within the course of a single laboratory experiment. Under selective conditions, this TE inactivated the uridine monophosphate synthase (UMPS) gene of P. tricornutum, one of the few endogenous genetic loci currently targeted for selectable auxotrophy for functional genetics and genome-editing applications. We report the observation of a recently mobilized transposon in diatoms with unique features. These include the combined presence of a MULE transposase with zinc-finger SWIM-type domains and a diatom-specific E3 ubiquitin ligase of the zinc-finger UBR type, which are suggestive of a mobilization mechanism. Our findings provide new elements for the understanding of the role of TEs in diatom genome evolution and in the enrichment of intraspecific genetic variability

Algebraic Characterization of Observability in Distance-Regular Consensus Networks

International audienceIn this paper, we study the observability issue in consensus networks modeled with strongly regular graphs or distance regular graphs. We derive a Kalman-like simple algebraic criterion for observability in distance regular graphs. This criterion consists in evaluating the rank of a matrix built with the components of the Bose-Mesner algebra associated with the considered graph. Then, we state a simple necessary condition of observability based on parameters of the graph, namely the diameter, the degree, and the number of vertices of the graph

Methyl jasmonate treatment affects the regulation of the 2-C-methyl-D-erythritol 4-phosphate pathway and early steps of the triterpenoid biosynthesis in Chlamydomonas reinhardtii

© 2019 Elsevier B.V. Terpenoids are a large and diverse class of naturally occurring metabolites serving many industrial applications and natural roles. Economically important terpenoids are often produced in low abundance from their natural sources, making their industrial-scale production challenging or uneconomical, therefore engineered microorganisms are frequently used as heterologous production platforms. Photosynthetic microorganisms, such as the green alga Chlamydomonas reinhardtii, represent promising systems to produce terpenoids in a cost-effective and sustainable manner, but knowledge about the regulation of their terpenoid metabolism remains limited. Here we report on the investigation of the phytohormone methyl jasmonate (MeJA) as elicitor of algal terpenoid synthesis. We treated C. reinhardtii cells in mid-exponential growth phase with three different concentrations of MeJA (0.05, 0.5 and 1 mM). The highest concentration of MeJA affected the photosynthetic activity of the cells, arrested the growth and up-regulated key genes of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, leading to a significant increase in intermediates of this pathway, squalene and (S)-2,3-epoxysqualene, while the abundance of cycloartenol, and two main sterols (ergosterol and 7-dehydroporiferasterol) decreased. These data suggest the redirection of the carbon flux towards the synthesis of yet uncharacterised triterpenoid secondary metabolites upon MeJA treatment. Our results offer important new insights into the regulation of the triterpenoid metabolism in C. reinhardtii and raise important questions on hormonal signalling in microalgae. Phytohormone treatment is tested for the first time in algae, where it holds great potential for identifying key transcriptional regulators of the MEP pathway as targets for future metabolic engineering studies for improve production of high-value triterpenoids

Impacts of mixing on foaming, methane production, stratification and microbial community in full-scale anaerobic co-digestion process

© 2019 Elsevier Ltd This study investigated the impact of mixing on key factors including foaming, substrate stratification, methane production and microbial community in three full scale anaerobic digesters. Digester foaming was observed at one plant that co-digested sewage sludge and food waste, and was operated without mixing. The lack of mixing led to uneven distribution of total chemical oxygen demand (tCOD) and volatile solid (VS) as well as methane production within the digester. 16S rRNA gene-based community analysis clearly differentiated the microbial community from the top and bottom. By contrast, foaming and substrate stratification were not observed at the other two plants with internal circulation mixing. The abundance of methanogens (Methanomicrobia) at the top was about four times higher than at the bottom, correlating to much higher methane production from the top verified by ex-situ biomethane assay, causing foaming. This result is consistent with foaming potential assessment of digestate samples from the digester

Driver-Node based Security Analysis for Network Controllability

In the study of network controllability, because driver nodes are vulnerable to control hijack and removals, and harmfulness of removing a driver node is still unknown. Therefore, to defend against such attacks, we identify each vertex of all minimum sets of driver nodes firstly. Also, to know the harmfulness of removing a driver node, we classify those identified nodes by impacts of removing a driver node on the minimum set of driver nodes to control the residual network. By the minimum input theorem, given a digraph, these two issues are respectively solved by finding each vertex that is an unmatched node related to a maximum matching, and classifying it by the impact of its removal on the number of unmatched nodes of the residual digraph. As a result, our driver-node identification and classification are executed in more efficient polynomial time than related works