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

A Lightweight Blockchain and Fog-enabled Secure Remote Patient Monitoring System

IoT has enabled the rapid growth of smart remote healthcare applications. These IoT-based remote healthcare applications deliver fast and preventive medical services to patients at risk or with chronic diseases. However, ensuring data security and patient privacy while exchanging sensitive medical data among medical IoT devices is still a significant concern in remote healthcare applications. Altered or corrupted medical data may cause wrong treatment and create grave health issues for patients. Moreover, current remote medical applications' efficiency and response time need to be addressed and improved. Considering the need for secure and efficient patient care, this paper proposes a lightweight Blockchain-based and Fog-enabled remote patient monitoring system that provides a high level of security and efficient response time. Simulation results and security analysis show that the proposed lightweight blockchain architecture fits the resource-constrained IoT devices well and is secure against attacks. Moreover, the augmentation of Fog computing improved the responsiveness of the remote patient monitoring system by 40%.Comment: 32 pages, 13 figures, 5 tables, accepted by Elsevier "Internet of Things; Engineering Cyber Physical Human Systems" journal on January 9, 202

Labour and Geography in Ireland, 2006 Evaluating the National Spatial Strategy for Ireland 2002 - 2020: People, Places and Potential

This Ph.D. identifies the spatial structures associated with Ireland’s economic geography through an analysis of travel-to-work patterns. In doing so it applies, within the Irish context, novel techniques to identify local labour market areas using data that, heretofore, were unavailable to researchers in Ireland, i.e. detailed spatial interaction data describing the journey to work. The primary aim of this thesis is to address a research lacuna concerning labour and labour market areas within the field of economic geography in Ireland. This research augments our understanding of the spatial structure of Ireland’s economy through the identification of local labour market areas and elucidates the geographies of who works where and places these within an international context. This, in turn, facilitates a detailed evaluation of Ireland’s ‘National Spatial Strategy 2002 – 2020: People, Places and Potential’ (NSS). The content of this strategy raises fundamental geographic questions concerning who lives where, where they work and the spatial structure of those functional areas associated with cities and towns in Ireland. The thesis explores these issues through the dual conceptual lenses of geographies of labour and labour geographies. In additional to these theoretical considerations, the research is guided by three broad objectives: a) the identification of local labour market areas, b) to enhance the effectiveness of spatial policies in Ireland concerned with economic development in general and those affecting labour processes in particular by critically engaging with the concept of polycentricity, and c) to empirically evaluate selected spatial concepts that are central to the NSS. In addressing these objectives the thesis makes a significant contribution to both economic geography and spatial planning. It provides a comprehensive evaluation of the NSS and provides new insights into the geography of local labour market areas in Ireland, whilst also providing a methodology that overcomes the central criticism of the technique used in previous studies identifying labour market areas

Building the Future Internet through FIRE

The Internet as we know it today is the result of a continuous activity for improving network communications, end user services, computational processes and also information technology infrastructures. The Internet has become a critical infrastructure for the human-being by offering complex networking services and end-user applications that all together have transformed all aspects, mainly economical, of our lives. Recently, with the advent of new paradigms and the progress in wireless technology, sensor networks and information systems and also the inexorable shift towards everything connected paradigm, first as known as the Internet of Things and lately envisioning into the Internet of Everything, a data-driven society has been created. In a data-driven society, productivity, knowledge, and experience are dependent on increasingly open, dynamic, interdependent and complex Internet services. The challenge for the Internet of the Future design is to build robust enabling technologies, implement and deploy adaptive systems, to create business opportunities considering increasing uncertainties and emergent systemic behaviors where humans and machines seamlessly cooperate

Stations as Nodes:

At the main point of intersection between the railway and the city, stations are key elements in the organization of the intermodal transport as well as catalysts of urban developments in metropolises, medium and small cities. The focus of this publication is to explore the enrichment of a renewed approach of railway stations as intermodal nodes, therefore acting as breeding grounds for both urban and social developments. This book has been initiated and built upon several activities currently running at the Amsterdam Institute for Advanced Metropolitan Solutions (AMS Institute), Delft University of Technology (DIMI, Delft Deltas Infrastructure Mobility Initiative and Department of Architecture of the Faculty of Architecture and the Built Environment) and University of Paris-Est (l’École d’Urbanisme de Paris). These activities have been framed within the context of two rapidly developing metropolitan areas: Randstad in the Netherlands and Métropole du Grand Paris in the Ile de France. This volume forms the basis for a research on the ‘role of stations in future metropolitan areas’ with the ambition to link the two countries, learning from their different cities and distinct geographical context through comparable mobility challenges on the levels of the inner city, suburban and peripheral areas. In line with these considerations, in 2018 AMS Institute, TU Delft/ DIMI and the Dutch Embassy in Paris with Atelier Néerlandais organized a successful workshop: ‘Stations of the Future’, in collaboration with La Fabrique de la Cité. Together with Dutch and French planning entities, involving mass transit operators and railway companies, this workshop focused on several case studies in both metropolitan areas to understand the role of station hubs as intermodal nodes. During this joint French-Dutch event that took place in Paris, we spoke on topics like Station as intermodal node, Station as destination and Station as data center, including a debate on the relation between public space and architecture, densification and programming of station areas, pedestrian flows management and the integration of data. Following the Paris workshop, the summer school ‘Integrated Mobility Challenges in Future Metropolitan Areas’ was organised by AMS Institute and Delft University of Technology/DIMI with the collaboration of the ARENA architectural research network, University of Paris-Est and the City of Amsterdam. This 8-day workshop extended the debate among international young professionals, academics and master students by looking at an important rail-metro node in the metropolitan area of the city Amsterdam: Sloterdijk Station – a crucial hub in a bigger urban area for mobility and exchange, and for urban growth. The main question was: which approaches and scenarios can be tested and applied to these intermodal nodes, particularly when dealing with lack of space and growing number of users? The results were four very different plans to improve the Sloterdijk Station area and to make the station a ‘future proof’ intermodal hub. In this publication, invited experts from practice and knowledge institutes in France and the Netherlands share their common experience and draw on specific aspects and problems of conception, management and development of stations. A brief overview of the results of the two initiatives ‘Stations of the Future’ and the summer school ‘Integrated Mobility Challenges in Future Metropolitan Areas’ is here illustrated, accompanied by photo reportages of both events and by a curated reportage of the Amsterdam Sloterdijk station area

Stations as Nodes

At the main point of intersection between the railway and the city, stations are key elements in the organization of the intermodal transport as well as catalysts of urban developments in metropolises, medium and small cities. The focus of this publication is to explore the enrichment of a renewed approach of railway stations as intermodal nodes, therefore acting as breeding grounds for both urban and social developments. This book has been initiated and built upon several activities currently running at the Amsterdam Institute for Advanced Metropolitan Solutions (AMS Institute), Delft University of Technology (DIMI, Delft Deltas Infrastructure Mobility Initiative and Department of Architecture of the Faculty of Architecture and the Built Environment) and University of Paris-Est (l’École d’Urbanisme de Paris). These activities have been framed within the context of two rapidly developing metropolitan areas: Randstad in the Netherlands and Métropole du Grand Paris in the Ile de France. This volume forms the basis for a research on the ‘role of stations in future metropolitan areas’ with the ambition to link the two countries, learning from their different cities and distinct geographical context through comparable mobility challenges on the levels of the inner city, suburban and peripheral areas. In line with these considerations, in 2018 AMS Institute, TU Delft/ DIMI and the Dutch Embassy in Paris with Atelier Néerlandais organized a successful workshop: ‘Stations of the Future’, in collaboration with La Fabrique de la Cité. Together with Dutch and French planning entities, involving mass transit operators and railway companies, this workshop focused on several case studies in both metropolitan areas to understand the role of station hubs as intermodal nodes. During this joint French-Dutch event that took place in Paris, we spoke on topics like Station as intermodal node, Station as destination and Station as data center, including a debate on the relation between public space and architecture, densification and programming of station areas, pedestrian flows management and the integration of data. Following the Paris workshop, the summer school ‘Integrated Mobility Challenges in Future Metropolitan Areas’ was organised by AMS Institute and Delft University of Technology/DIMI with the collaboration of the ARENA architectural research network, University of Paris-Est and the City of Amsterdam. This 8-day workshop extended the debate among international young professionals, academics and master students by looking at an important rail-metro node in the metropolitan area of the city Amsterdam: Sloterdijk Station – a crucial hub in a bigger urban area for mobility and exchange, and for urban growth. The main question was: which approaches and scenarios can be tested and applied to these intermodal nodes, particularly when dealing with lack of space and growing number of users? The results were four very different plans to improve the Sloterdijk Station area and to make the station a ‘future proof’ intermodal hub. In this publication, invited experts from practice and knowledge institutes in France and the Netherlands share their common experience and draw on specific aspects and problems of conception, management and development of stations. A brief overview of the results of the two initiatives ‘Stations of the Future’ and the summer school ‘Integrated Mobility Challenges in Future Metropolitan Areas’ is here illustrated, accompanied by photo reportages of both events and by a curated reportage of the Amsterdam Sloterdijk station area

Building the Future Internet through FIRE

The Internet as we know it today is the result of a continuous activity for improving network communications, end user services, computational processes and also information technology infrastructures. The Internet has become a critical infrastructure for the human-being by offering complex networking services and end-user applications that all together have transformed all aspects, mainly economical, of our lives. Recently, with the advent of new paradigms and the progress in wireless technology, sensor networks and information systems and also the inexorable shift towards everything connected paradigm, first as known as the Internet of Things and lately envisioning into the Internet of Everything, a data-driven society has been created. In a data-driven society, productivity, knowledge, and experience are dependent on increasingly open, dynamic, interdependent and complex Internet services. The challenge for the Internet of the Future design is to build robust enabling technologies, implement and deploy adaptive systems, to create business opportunities considering increasing uncertainties and emergent systemic behaviors where humans and machines seamlessly cooperate