Node-to-node and node-to-medium synchronization in quorum sensing networks affected by state-dependent noise

A quorum sensing network is a form of communication system where nodes talk to each other through a shared environment or medium. Such networks arise in many applications, such as bacterial quorum sensing, where diffusing signaling molecules are exchanged with the extracellular environment, and in social networks, where decisions might be influenced by social media. In this paper, we analyze node-to-node and node-to-medium synchronization in these quorum sensing networks when nodes are affected by relative-state-dependent noise and the medium has a different dynamics from the nodes. By using stochastic Lyapunov arguments, we give a number of sufficient conditions for the stability of the synchronization manifold and compare the synchronization dynamics induced by common (extrinsic) noise and independent (intrinsic) noise. We also carry out a stochastic phase plane analysis of the dynamics on the synchronization manifold by introducing the notion of a stochastic invariant manifold. (The PDF has been corrected.

Symmetries, Stability, and Control in Nonlinear Systems and Networks

This paper discusses the interplay of symmetries and stability in the analysis and control of nonlinear dynamical systems and networks. Specifically, it combines standard results on symmetries and equivariance with recent convergence analysis tools based on nonlinear contraction theory and virtual dynamical systems. This synergy between structural properties (symmetries) and convergence properties (contraction) is illustrated in the contexts of network motifs arising e.g. in genetic networks, of invariance to environmental symmetries, and of imposing different patterns of synchrony in a network.Comment: 16 pages, second versio

Opinion Behavior Analysis in Social Networks Under the Influence of Coopetitive Media

Both interpersonal communication and media contact are important information sources and play a significant role in shaping public opinions of large populations. In this paper, we investigate how the opinion-forming process evolves over social networks under the media influence. In addition to being affected by the opinions of their connected peers, the media cooperate and/or compete mutually with each other. Networks with mixed cooperative and competitive interactions are said to be coopetitive . In this endeavor, a novel mathematical model of opinion dynamics is introduced, which captures the information diffusion process under consideration, makes use of the community-based network structure, and takes into account personalized biases among individuals in social networks. By employing port-Hamiltonian system theory to analyze the modeled opinion dynamics, we predict how public opinions evolve in the long run through social entities and find applications in political strategy science. A key technical observation is that as a result of the port-Hamiltonian formulation, the mathematical passivity property of individuals’ self-dynamics facilitates the convergence analysis of opinion evolution. We explain how to steer public opinions towards consensus, polarity, or neutrality, and investigate how an autocratic media coalition might emerge regardless of public views. We also assess the role of interpersonal communication and media exposure, which in itself is an essential topic in mathematical sociology

Data based identification and prediction of nonlinear and complex dynamical systems

We thank Dr. R. Yang (formerly at ASU), Dr. R.-Q. Su (formerly at ASU), and Mr. Zhesi Shen for their contributions to a number of original papers on which this Review is partly based. This work was supported by ARO under Grant No. W911NF-14-1-0504. W.-X. Wang was also supported by NSFC under Grants No. 61573064 and No. 61074116, as well as by the Fundamental Research Funds for the Central Universities, Beijing Nova Programme.Peer reviewedPostprin

Complex and unexpected dynamics in simple genetic regulatory networks

Peer reviewedPublisher PD

A synthetic gene network architecture that propagates

Thesis (Ph.D.)--Boston UniversitySynthetic biology is a field that is tending towards maturity. Synthetic gene networks are becoming increasingly more complex, and are being engineered with functional outcomes as design goals rather than just logical demonstration. As complex as circuits become, it is still a difficult process to build a functional gene network. Much work has been done to reduce DNA assembly time, but none specifically addresses the complexity ofproducing functional networks. To this end, we present a synthetic gene network assembly strategy that emphasizes characterization-driven iteration. The Plug- and-Play methodology allows for post-construction modification to circuits, which enables the simple swapping of parts. This type of modification makes it possible to tune circuits for troubleshooting, or even to repurpose networks. We used a specified set of restriction enzymes, a library of optimized parts and a compatible backbone vector system to preserve uniqueness of cloning sites and allow maintained post-construction access to the network. To demonstrate the system, we rapidly constructed a bistable genetic toggle and subsequently transformed it into two functionally distinct networks, a 3 and 4-node feed-forward loop. We also designed a synthetic gene network that can propagate signals across a population ofisogenic bacteria. We used the Plug-and-Play methodology to quickly construct an excitable system that toggles between sending and receiving states. We developed a spatial assay platform that could accommodate long-term, large-scale plating experiments so as to visualize the propagation effect on the centimeter scale. We built several iterations ofthe propagating network, probed the regulatory dynamics ofthe various nodes and identified problematic nodes. We took steps to address these nodes with both orthogonal transcription machinery as well as multiple modes of genetic regulation. We integrated the propagating networks with a DNA-damage sensitive triggering module. This opened up the gene network to potentially complex applications such as antibiotic sensing, or longer-distance communication experiments

Analysis of MAC Strategies for Underwater Acoustic Networks

En esta tesis presentamos los protocolos MAC diseñados para redes acústicas subacuáticas, clasificándolos en amplias categorías, proporcionando técnicas de medición de rendimiento y análisis comparativo para seleccionar el mejor algoritmo MAC para aplicaciones específicas. Floor Acquisition Multiple Access (FAMA) es un protocolo MAC que se propuso para redes acústicas submarinas como medio para resolver los problemas de terminales ocultos y expuestos. Una versión modificada, Slotted FAMA, tenía como objetivo proporcionar ahorros de energía mediante el uso de ranuras de tiempo, eliminando así la necesidad de paquetes de control excesivamente largos en FAMA. Sin embargo, se ha observado que, debido al alto retraso de propagación en estas redes, el coste de perder un ACK es muy alto y tiene un impacto significativo en el rendimiento. Los mecanismos MultiACK y EarlyACK han sido analizados para el protocolo MACA, para mejorar su eficiencia. El mecanismo MultiACK aumenta la probabilidad de recibir al menos un paquete ACK al responder con un tren de paquetes ACK, mientras que el mecanismo EarlyACK evita la repetición de todo el ciclo de contención y transmisión de datos RTS / CTS enviando un ACK temprano. En esta investigación se presenta un análisis matemático de las dos variantes, los mecanismos MultiACK y EarlyACK, en Slotted FAMA. La investigación incluye las expresiones analíticas modificadas así como los resultados numéricos. Las simulaciones se llevaron a cabo utilizando ns-3. Los resultados han sido probados y validados utilizando Excel y MATLAB. La evaluación del rendimiento de S-FAMA con dos variantes mostró un factor de mejora del 65,05% en la probabilidad de recibir un ACK correctamente utilizando el mecanismo MultiACK y del 60,58% en la prevención de la repetición del ciclo completo, con EarlyACK. El impacto de este factor de mejora en el retardo, el tamaño del paquete de datos y el rendimiento también se analiza. La energía de transmisión desperdiciada y consumida en los mecanismos MultiACK y EarlyACK se analizan y comparan con S-FAMA. El rendimiento se ha evaluado, alcanzando una mejora en ambos casos, en comparación con S-FAMA. Estos mecanismos tendrán una utilidad práctica en caso de pérdida de ACK, al ahorrar energía y tiempo en períodos críticos. Fecha de lectura de Tesis Doctoral: 28 septiembre 2018.Esta tesis presenta una investigación sobre los protocolos MAC utilizados en la comunicación subacuática para explorar el mundo submarino. Los protocolos MAC ayudan en el acceso al medio compartido y la recopilación de datos de los océanos, para monitorizar el clima y la contaminación, la prevención de catástrofes, la navegación asistida, la vigilancia estratégica y la exploración de los recursos minerales. Esta investigación beneficiará a sectores como las industrias militares, de petróleo y gas, pesquerías, compañías de instrumentación subacuática, organismos de investigación, etc. El protocolo MAC afecta la vida útil de las redes inalámbricas de sensores. La eficiencia energética de las redes acústicas submarinas se ve gravemente afectada por las propiedades típicas de la propagación de las ondas acústicas. Los largos retrasos de propagación y las colisiones de paquetes de datos dificultan la transmisión de los paquetes de datos, que contienen información útil para que los usuarios realicen tareas de supervisión colectivas. El objetivo de este estudio es proponer nuevos mecanismos para protocolos MAC diseñados para funcionar en redes acústicas submarinas, con el propósito de mejorar su rendimiento. Para alcanzar ese objetivo es necesario realizar un análisis comparativo de los protocolos existentes. Lo que además sienta un procedimiento metodológicamente correcto para realizar esa comparación. Como la comunicación subacuática depende de ondas acústicas, en el diseño de los protocolos de MAC submarinos surgen varios desafíos como latencia prolongada, ancho de banda limitado, largas demoras en la propagación, grandes tasas de error de bit, pérdidas momentáneas en las conexiones, severo efecto multicamino y desvanecimientos. Los protocolos MAC terrestres, si se implementan directamente, funcionarán de manera ineficiente

Error control in bacterial quorum communications

Quorum sensing (QS) is used to describe the communication between bacterial cells, whereby a coordinated population response is controlled through the synthesis, accumulation and subsequent sensing of specific diffusible chemical signals called autoinducers, enabling a cluster of bacteria to regulate gene expression and behavior collectively and synchronously, and assess their own population. As a promising method of molecular communication (MC), bacterial populations can be programmed as bio-transceivers to establish information transmission using molecules. In this work, to investigate the key features for MC, a bacterial QS system is introduced, which contains two clusters of bacteria, specifically Vibrio fischeri, as the transmitter node and receiver node, and the diffusive channel. The transmitted information is represented by the concentration of autoinducers with on-off keying (OOK) modulation. In addition, to achieve better reliability and energy efficiency, different error control techniques, including forward error correction (FEC) and Automatic Repeat reQuest (ARQ) are taken into consideration. For FEC, this work presents a comparison of the performance of traditional Hamming codes, Minimum Energy Codes (MEC) and Luby Transform (LT) codes over the channel. In addition, it applied several ARQ protocols, namely Stop-N-Wait (SW-ARQ), Go-Back-N (GBN-ARQ), and Selective-Repeat (SR-ARQ) combined with error detection codes to achieve better reliability. Results show that both the FEC and ARQ techniques can enhance the channel reliability, and that ARQ can resolve the issue of out-of-sequence and duplicate packet delivery. Moreover, this work further addresses the question of optimal frame size for data communication in this channel capacity and energy constrained bacterial quorum communication system. A novel energy model which is constructed using the experimental validated synthetic logic gates has been proposed to help with the optimization process. The optimal fixed frame length is determined for a set of channel parameters by maximizing the throughput and energy efficiency matrix

Secure Routing in Wireless Mesh Networks

Wireless mesh networks (WMNs) have emerged as a promising concept to meet the challenges in next-generation networks such as providing flexible, adaptive, and reconfigurable architecture while offering cost-effective solutions to the service providers. Unlike traditional Wi-Fi networks, with each access point (AP) connected to the wired network, in WMNs only a subset of the APs are required to be connected to the wired network. The APs that are connected to the wired network are called the Internet gateways (IGWs), while the APs that do not have wired connections are called the mesh routers (MRs). The MRs are connected to the IGWs using multi-hop communication. The IGWs provide access to conventional clients and interconnect ad hoc, sensor, cellular, and other networks to the Internet. However, most of the existing routing protocols for WMNs are extensions of protocols originally designed for mobile ad hoc networks (MANETs) and thus they perform sub-optimally. Moreover, most routing protocols for WMNs are designed without security issues in mind, where the nodes are all assumed to be honest. In practical deployment scenarios, this assumption does not hold. This chapter provides a comprehensive overview of security issues in WMNs and then particularly focuses on secure routing in these networks. First, it identifies security vulnerabilities in the medium access control (MAC) and the network layers. Various possibilities of compromising data confidentiality, data integrity, replay attacks and offline cryptanalysis are also discussed. Then various types of attacks in the MAC and the network layers are discussed. After enumerating the various types of attacks on the MAC and the network layer, the chapter briefly discusses on some of the preventive mechanisms for these attacks.Comment: 44 pages, 17 figures, 5 table