Nature-Inspired Interconnects for Self-Assembled Large-Scale Network-on-Chip Designs

Future nano-scale electronics built up from an Avogadro number of components needs efficient, highly scalable, and robust means of communication in order to be competitive with traditional silicon approaches. In recent years, the Networks-on-Chip (NoC) paradigm emerged as a promising solution to interconnect challenges in silicon-based electronics. Current NoC architectures are either highly regular or fully customized, both of which represent implausible assumptions for emerging bottom-up self-assembled molecular electronics that are generally assumed to have a high degree of irregularity and imperfection. Here, we pragmatically and experimentally investigate important design trade-offs and properties of an irregular, abstract, yet physically plausible 3D small-world interconnect fabric that is inspired by modern network-on-chip paradigms. We vary the framework's key parameters, such as the connectivity, the number of switch nodes, the distribution of long- versus short-range connections, and measure the network's relevant communication characteristics. We further explore the robustness against link failures and the ability and efficiency to solve a simple toy problem, the synchronization task. The results confirm that (1) computation in irregular assemblies is a promising and disruptive computing paradigm for self-assembled nano-scale electronics and (2) that 3D small-world interconnect fabrics with a power-law decaying distribution of shortcut lengths are physically plausible and have major advantages over local 2D and 3D regular topologies

Structure and topology of transcriptional regulatory networks and their applications in bio-inspired networking

Biological networks carry out vital functions necessary for sustenance despite environmental adversities. Transcriptional Regulatory Network (TRN) is one such biological network that is formed due to the interaction between proteins, called Transcription Factors (TFs), and segments of DNA, called genes. TRNs are known to exhibit functional robustness in the face of perturbation or mutation: a property that is proven to be a result of its underlying network topology. In this thesis, we first propose a three-tier topological characterization of TRN to analyze the interplay between the significant graph-theoretic properties of TRNs such as scale-free out-degree distribution, low graph density, small world property and the abundance of subgraphs called motifs. Specifically, we pinpoint the role of a certain three-node motif, called Feed Forward Loop (FFL) motif in topological robustness as well as information spread in TRNs. With the understanding of the TRN topology, we explore its potential use in design of fault-tolerant communication topologies. To this end, we first propose an edge rewiring mechanism that remedies the vulnerability of TRNs to the failure of well-connected nodes, called hubs, while preserving its other significant graph-theoretic properties. We apply the rewired TRN topologies in the design of wireless sensor networks that are less vulnerable to targeted node failure. Similarly, we apply the TRN topology to address the issues of robustness and energy-efficiency in the following networking paradigms: robust yet energy-efficient delay tolerant network for post disaster scenarios, energy-efficient data-collection framework for smart city applications and a data transfer framework deployed over a fog computing platform for collaborative sensing --Abstract, page iii

Self-Synchronization in Duty-cycled Internet of Things (IoT) Applications

In recent years, the networks of low-power devices have gained popularity. Typically these devices are wireless and interact to form large networks such as the Machine to Machine (M2M) networks, Internet of Things (IoT), Wearable Computing, and Wireless Sensor Networks. The collaboration among these devices is a key to achieving the full potential of these networks. A major problem in this field is to guarantee robust communication between elements while keeping the whole network energy efficient. In this paper, we introduce an extended and improved emergent broadcast slot (EBS) scheme, which facilitates collaboration for robust communication and is energy efficient. In the EBS, nodes communication unit remains in sleeping mode and are awake just to communicate. The EBS scheme is fully decentralized, that is, nodes coordinate their wake-up window in partially overlapped manner within each duty-cycle to avoid message collisions. We show the theoretical convergence behavior of the scheme, which is confirmed through real test-bed experimentation.Comment: 12 Pages, 11 Figures, Journa

A Chemistry-Inspired Framework for Achieving Consensus in Wireless Sensor Networks

The aim of this paper is to show how simple interaction mechanisms, inspired by chemical systems, can provide the basic tools to design and analyze a mathematical model for achieving consensus in wireless sensor networks, characterized by balanced directed graphs. The convergence and stability of the model are first proven by using new mathematical tools, which are borrowed directly from chemical theory, and then validated by means of simulation results, for different network topologies and number of sensors. The underlying chemical theory is also used to derive simple interaction rules that may account for practical issues, such as the estimation of the number of neighbors and the robustness against perturbations. Finally, the proposed chemical solution is validated under real-world conditions by means of a four-node hardware implementation where the exchange of information among nodes takes place in a distributed manner (with no need for any admission control and synchronism procedure), simply relying on the transmission of a pulse whose rate is proportional to the state of each sensor.Comment: 12 pages, 10 figures, submitted to IEEE Sensors Journa

Motifs Enable Communication Efficiency and Fault-Tolerance in Transcriptional Networks

Analysis of the topology of transcriptional regulatory networks (TRNs) is an effective way to study the regulatory interactions between the transcription factors (TFs) and the target genes. TRNs are characterized by the abundance of motifs such as feed forward loops (FFLs), which contribute to their structural and functional properties. In this paper, we focus on the role of motifs (specifically, FFLs) in signal propagation in TRNs and the organization of the TRN topology with FFLs as building blocks. To this end, we classify nodes participating in FFLs (termed motif central nodes) into three distinct roles (namely, roles A, B and C), and contrast them with TRN nodes having high connectivity on the basis of their potential for information dissemination, using metrics such as network efficiency, path enumeration, epidemic models and standard graph centrality measures. We also present the notion of a three tier architecture and how it can help study the structural properties of TRN based on connectivity and clustering tendency of motif central nodes. Finally, we motivate the potential implication of the structural properties of motif centrality in design of efficient protocols of information routing in communication networks as well as their functional properties in global regulation and stress response to study specific disease conditions and identification of drug targets

Self-synchronized duty-cycling for sensor networks with energy harvesting capabilities: Implementation in Wiselib

In this work we present a protocol for a self- synchronized duty-cycling mechanism in wireless sensor net- works with energy harvesting capabilities. The protocol is im- plemented in Wiselib, a library of generic algorithms for sensor networks. Simulations are conducted with the sensor network simulator Shawn. They are based on the specifications of real hardware known as iSense sensor nodes. The experimental results show that the proposed mechanism is able to adapt to changing energy availabilities. Moreover, it is shown that the system is very robust against packet loss.Postprint (published version

Memory and information processing in neuromorphic systems

A striking difference between brain-inspired neuromorphic processors and current von Neumann processors architectures is the way in which memory and processing is organized. As Information and Communication Technologies continue to address the need for increased computational power through the increase of cores within a digital processor, neuromorphic engineers and scientists can complement this need by building processor architectures where memory is distributed with the processing. In this paper we present a survey of brain-inspired processor architectures that support models of cortical networks and deep neural networks. These architectures range from serial clocked implementations of multi-neuron systems to massively parallel asynchronous ones and from purely digital systems to mixed analog/digital systems which implement more biological-like models of neurons and synapses together with a suite of adaptation and learning mechanisms analogous to the ones found in biological nervous systems. We describe the advantages of the different approaches being pursued and present the challenges that need to be addressed for building artificial neural processing systems that can display the richness of behaviors seen in biological systems.Comment: Submitted to Proceedings of IEEE, review of recently proposed neuromorphic computing platforms and system

Bio-inspired computation: where we stand and what's next

In recent years, the research community has witnessed an explosion of literature dealing with the adaptation of behavioral patterns and social phenomena observed in nature towards efficiently solving complex computational tasks. This trend has been especially dramatic in what relates to optimization problems, mainly due to the unprecedented complexity of problem instances, arising from a diverse spectrum of domains such as transportation, logistics, energy, climate, social networks, health and industry 4.0, among many others. Notwithstanding this upsurge of activity, research in this vibrant topic should be steered towards certain areas that, despite their eventual value and impact on the field of bio-inspired computation, still remain insufficiently explored to date. The main purpose of this paper is to outline the state of the art and to identify open challenges concerning the most relevant areas within bio-inspired optimization. An analysis and discussion are also carried out over the general trajectory followed in recent years by the community working in this field, thereby highlighting the need for reaching a consensus and joining forces towards achieving valuable insights into the understanding of this family of optimization techniques