Topological and Graph-coloring Conditions on the Parameter-independent Stability of Second-order Networked Systems

In this paper, we study parameter-independent stability in qualitatively heterogeneous passive networked systems containing damped and undamped nodes. Given the graph topology and a set of damped nodes, we ask if output consensus is achieved for all system parameter values. For given parameter values, an eigenspace analysis is used to determine output consensus. The extension to parameter-independent stability is characterized by a coloring problem, named the richly balanced coloring (RBC) problem. The RBC problem asks if all nodes of the graph can be colored red, blue and black in such a way that (i) every damped node is black, (ii) every black node has blue neighbors if and only if it has red neighbors, and (iii) not all nodes in the graph are black. Such a colored graph is referred to as a richly balanced colored graph. Parameter-independent stability is guaranteed if there does not exist a richly balanced coloring. The RBC problem is shown to cover another well-known graph coloring scheme known as zero forcing sets. That is, if the damped nodes form a zero forcing set in the graph, then a richly balanced coloring does not exist and thus, parameter-independent stability is guaranteed. However, the full equivalence of zero forcing sets and parameter-independent stability holds only true for tree graphs. For more general graphs with few fundamental cycles an algorithm, named chord node coloring, is proposed that significantly outperforms a brute-force search for solving the NP-complete RBC problem.Comment: 30 pages, accepted for publication in SICO

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

A methodology for the structural and functional analysis of signaling and regulatory networks

BACKGROUND: Structural analysis of cellular interaction networks contributes to a deeper understanding of network-wide interdependencies, causal relationships, and basic functional capabilities. While the structural analysis of metabolic networks is a well-established field, similar methodologies have been scarcely developed and applied to signaling and regulatory networks. RESULTS: We propose formalisms and methods, relying on adapted and partially newly introduced approaches, which facilitate a structural analysis of signaling and regulatory networks with focus on functional aspects. We use two different formalisms to represent and analyze interaction networks: interaction graphs and (logical) interaction hypergraphs. We show that, in interaction graphs, the determination of feedback cycles and of all the signaling paths between any pair of species is equivalent to the computation of elementary modes known from metabolic networks. Knowledge on the set of signaling paths and feedback loops facilitates the computation of intervention strategies and the classification of compounds into activators, inhibitors, ambivalent factors, and non-affecting factors with respect to a certain species. In some cases, qualitative effects induced by perturbations can be unambiguously predicted from the network scheme. Interaction graphs however, are not able to capture AND relationships which do frequently occur in interaction networks. The consequent logical concatenation of all the arcs pointing into a species leads to Boolean networks. For a Boolean representation of cellular interaction networks we propose a formalism based on logical (or signed) interaction hypergraphs, which facilitates in particular a logical steady state analysis (LSSA). LSSA enables studies on the logical processing of signals and the identification of optimal intervention points (targets) in cellular networks. LSSA also reveals network regions whose parametrization and initial states are crucial for the dynamic behavior. We have implemented these methods in our software tool CellNetAnalyzer (successor of FluxAnalyzer) and illustrate their applicability using a logical model of T-Cell receptor signaling providing non-intuitive results regarding feedback loops, essential elements, and (logical) signal processing upon different stimuli. CONCLUSION: The methods and formalisms we propose herein are another step towards the comprehensive functional analysis of cellular interaction networks. Their potential, shown on a realistic T-cell signaling model, makes them a promising tool

Fundamentals of Large Sensor Networks: Connectivity, Capacity, Clocks and Computation

Sensor networks potentially feature large numbers of nodes that can sense their environment over time, communicate with each other over a wireless network, and process information. They differ from data networks in that the network as a whole may be designed for a specific application. We study the theoretical foundations of such large scale sensor networks, addressing four fundamental issues- connectivity, capacity, clocks and function computation. To begin with, a sensor network must be connected so that information can indeed be exchanged between nodes. The connectivity graph of an ad-hoc network is modeled as a random graph and the critical range for asymptotic connectivity is determined, as well as the critical number of neighbors that a node needs to connect to. Next, given connectivity, we address the issue of how much data can be transported over the sensor network. We present fundamental bounds on capacity under several models, as well as architectural implications for how wireless communication should be organized. Temporal information is important both for the applications of sensor networks as well as their operation.We present fundamental bounds on the synchronizability of clocks in networks, and also present and analyze algorithms for clock synchronization. Finally we turn to the issue of gathering relevant information, that sensor networks are designed to do. One needs to study optimal strategies for in-network aggregation of data, in order to reliably compute a composite function of sensor measurements, as well as the complexity of doing so. We address the issue of how such computation can be performed efficiently in a sensor network and the algorithms for doing so, for some classes of functions.Comment: 10 pages, 3 figures, Submitted to the Proceedings of the IEE