Towards intelligent aquaculture. Development of an early Biological Warning System to monitor exposure to contaminants and fish welfare: from artificial vision to systems modelling

161 p.

A Task-Graph Execution Manager for Reconfigurable Multi-tasking Systems

Reconfigurable hardware can be used to build multi tasking systems that dynamically adapt themselves to the requirements of the running applications. This is especially useful in embedded systems, since the available resources are very limited and the reconfigurable hardware can be reused for different applications. In these systems computations are frequently represented as task graphs that are executed taking into account their internal dependencies and the task schedule. The management of the task graph execution is critical for the system performance. In this regard, we have developed two dif erent versions, a software module and a hardware architecture, of a generic task-graph execution manager for reconfigurable multi-tasking systems. The second version reduces the run-time management overheads by almost two orders of magnitude. Hence it is especially suitable for systems with exigent timing constraints. Both versions include specific support to optimize the reconfiguration process.

Adaptivity and a posteriori error control for bifurcation problems II: Incompressible fluid flow in open systems with Z_2 symmetry

In this article we consider the a posteriori error estimation and adaptive mesh refinement of discontinuous Galerkin finite element approximations of the bifurcation problem associated with the steady incompressible Navier-Stokes equations. Particular attention is given to the reliable error estimation of the critical Reynolds number at which a steady pitchfork or Hopf bifurcation occurs when the underlying physical system possesses reflectional or Z_2 symmetry. Here, computable a posteriori error bounds are derived based on employing the generalization of the standard Dual-Weighted-Residual approach, originally developed for the estimation of target functionals of the solution, to bifurcation problems. Numerical experiments highlighting the practical performance of the proposed a posteriori error indicator on adaptively refined computational meshes are presented.

Intrusion Detection Systems in SDN-based Self-Healing PMU Networks

Nowadays, Power grids are critical infrastructures on which everything else relies, and their correct behavior is of the highest priority. New smart devices are being deployed to be able to manage and control power grids more efficiently and avoid instability. However, the deployment of such smart devices like Phasor Measurement Units (PMU) and Phasor Data Concentrators (PDC), open new opportunities for cyber attackers to exploit network vulnerabilities. If a PDC is compromised, all data coming from PMUs to that PDC is lost, reducing network observability. Our approach to solve this problem is to develop an Intrusion detection System (IDS) in a Software-defined network (SDN). allowing the IDS system to detect compromised devices and use that information as an input for a self-healing SDN controller, which redirects the data of the PMUs to a new, uncompromised PDC, maintaining the maximum possible network observability at every moment. During this research, we have successfully implemented Self-healing in an example network with an SDN controller based on Ryu controller. We have also assessed intrinsic vulnerabilities of Wide Area Management Systems (WAMS) and SCADA networks, and developed some rules for the Intrusion Detection system which specifically protect vulnerabilities of these networks. The integration of the IDS and the SDN controller was also successful. \\To achieve this goal, the first steps will be to implement an existing Self-healing SDN controller and assess intrinsic vulnerabilities of Wide Area Measurement Systems (WAMS) and SCADA networks. After that, we will integrate the Ryu controller with Snort, and create the Snort rules that are specific for SCADA or WAMS systems and protocols.

Disorder driven transitions in non-equilibrium quantum systems

This thesis presents studies of the role of disorder in non-equilibrium quantum systems. The quantum states relevant to dynamics in these systems are very different from the ground state of the Hamiltonian. Two distinct systems are studied, (i) periodically driven Hamiltonians in two dimensions, and (ii) electrons in a one-dimensional lattice with power-law decaying hopping amplitudes. In the first system, the novel phases that are induced from the interplay of periodic driving, topology and disorder are studied. In the second system, the Anderson transition in all the eigenstates of the Hamiltonian are studied, as a function of the power-law exponent of the hopping amplitude.

In periodically driven systems the study focuses on the effect of disorder in the nature of the topology of the steady states. First, we investigate the robustness to disorder of Floquet topological insulators (FTIs) occurring in semiconductor quantum wells. Such FTIs are generated by resonantly driving a transition between the valence and conduction band. We show that when disorder is added, the topological nature of such FTIs persists as long as there is a gap at the resonant quasienergy. For strong enough disorder, this gap closes and all the states become localized as the system undergoes a transition to a trivial insulator.

Interestingly, the effects of disorder are not necessarily adverse, disorder can also induce a transition from a trivial to a topological system, thereby establishing a Floquet Topological Anderson Insulator (FTAI). Such a state would be a dynamical realization of the topological Anderson insulator. We identify the conditions on the driving field necessary for observing such a transition. We realize such a disorder induced topological Floquet spectrum in the driven honeycomb lattice and quantum well models.

Finally, we show that two-dimensional periodically driven quantum systems with spatial disorder admit a unique topological phase, which we call the anomalous Floquet-Anderson insulator (AFAI). The AFAI is characterized by a quasienergy spectrum featuring chiral edge modes coexisting with a fully localized bulk. Such a spectrum is impossible for a time-independent, local Hamiltonian. These unique characteristics of the AFAI give rise to a new topologically protected nonequilibrium transport phenomenon: quantized, yet nonadiabatic, charge pumping. We identify the topological invariants that distinguish the AFAI from a trivial, fully localized phase, and show that the two phases are separated by a phase transition.

The thesis also present the study of disordered systems using Wegner's Flow equations. The Flow Equation Method was proposed as a technique for studying excited states in an interacting system in one dimension. We apply this method to a one-dimensional tight binding problem with power-law decaying hoppings. This model presents a transition as a function of the exponent of the decay. It is shown that the the entire phase diagram, i.e. the delocalized, critical and localized phases in these systems can be studied using this technique. Based on this technique, we develop a strong-bond renormalization group that procedure where we solve the Flow Equations iteratively. This renormalization group approach provides a new framework to study the transition in this system.

DIFFUSE-INTERFACE FIELD APPROACH TO MODELING SELF-ASSEMBLY OF HETEROGENEOUS COLLOIDAL SYSTEMS AND RELATED DIPOLE-DIPOLE INTERACTION PHENOMENA

Colloid self-assembly under external control is a new route to fabrication of advanced materials with novel microstructures and appealing functionalities. The kinetic processes of colloidal self-assembly have attracted great interests also because they are similar to many atomic level kinetic processes of materials. In the past decades, rapid technological progresses have been achieved on producing shape-anisotropic, patchy, core-shell structured particles and particles with electric/magnetic charges/dipoles, which greatly enriched the self-assembled structures. Multi-phase carrier liquids offer new route to controlling colloidal self-assembly. Therefore, heterogeneity is the essential characteristics of colloid system, while so far there still lacks a model that is able to efficiently incorporate these possible heterogeneities. This thesis is mainly devoted to development of a model and computational study on the complex colloid system through a diffuse-interface field approach (DIFA), recently developed by Wang et al. This meso-scale model is able to describe arbitrary particle shape and arbitrary charge/dipole distribution on the surface or body of particles. Within the framework of DIFA, a Gibbs-Duhem-type formula is introduced to treat Laplace pressure in multi-liquid-phase colloidal system and it obeys Young-Laplace equation. The model is thus capable to quantitatively study important capillarity related phenomena. Extensive computer simulations are performed to study the fundamental behavior of heterogeneous colloidal system. The role of Laplace pressure is revealed in determining the mechanical equilibrium of shape-anisotropic particles at fluid interfaces. In particular, it is found that the Laplace pressure plays a critical role in maintaining the stability of capillary bridges between close particles, which sheds light on a novel route to in situ firming compact but fragile colloidal microstructures via capillary bridges. Simulation results also show that competition between like-charge repulsion, dipole-dipole interaction and Brownian motion dictates the degree of aggregation of heterogeneously charged particles. Assembly and alignment of particles with magnetic dipoles under external field is studied. Finally, extended studies on the role of dipole-dipole interaction are performed for ferromagnetic and ferroelectric domain phenomena. The results reveal that the internal field generated by dipoles competes with external field to determine the dipole-domain evolution in ferroic materials.

Understanding ten-eleven translocation-2 in hematological and nervous systems

I proposed the study of two distinct aspects of Ten-Eleven Translocation 2 (TET2) protein for understanding specific functions in different body systems. ^ In Part I, I characterized the molecular mechanisms of Tet2 in the hematological system. As the second member of Ten-Eleven Translocation protein family, TET2 is frequently mutated in leukemic patients. Previous studies have shown that the TET2 mutations frequently occur in 20% myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN), 10% T-cell lymphoma leukemia and 2% B-cell lymphoma leukemia. Genetic mouse models also display distinct phenotypes of various types of hematological malignancies. I performed 5-hydroxymethylcytosine (5hmC) chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) of hematopoietic stem/progenitor cells to determine whether the deletion of Tet2 can affect the abundance of 5hmC at myeloid, T-cell and B-cell specific gene transcription start sites, which ultimately result in various hematological malignancies. Subsequent Exome sequencing (Exome-Seq) showed that disease-specific genes are mutated in different types of tumors, which suggests that TET2 may protect the genome from being mutated. The direct interaction between TET2 and Mutator S Homolog 6 (MSH6) protein suggests TET2 is involved in DNA mismatch repair. Finally, in vivo mismatch repair studies show that the loss of Tet2 causes a mutator phenotype. Taken together, my data indicate that TET2 binds to MSH6 to protect genome integrity. ^ In Part II, I intended to better understand the role of Tet2 in the nervous system. 5-hydroxymethylcytosine regulates epigenetic modification during neurodevelopment and aging. Thus, Tet2 may play a critical role in regulating adult neurogenesis. To examine the physiological significance of Tet2 in the nervous system, I first showed that the deletion of Tet2 reduces the 5hmC levels in neural stem cells. Mice lacking Tet2 show abnormal hippocampal neurogenesis along with 5hmC alternations at different gene promoters and corresponding gene expression downregulation. Through the luciferase reporter assay, two neural factors Neurogenic differentiation 1 (NeuroD1) and Glial fibrillary acidic protein (Gfap) were down-regulated in Tet2 knockout cells. My results suggest that Tet2 regulates neural stem/progenitor cell proliferation and differentiation in adult brain.^

DIGITAL HISTORY: DESIGNING VIRTUAL ENVIRONMENTS THAT SUPPORT CRITICAL THINKING AND IDEA EXCHANGE, MOTIVATE AND ENGAGE USERS

Thesis (Master, Education) -- Queen's University, 2016-08-29 15:56:53.748

Water sorption-induced crystallization, structural relaxations and strength analysis of relaxation times in amorphous lactose/whey protein systems

Water sorption-induced crystallization, α-relaxations and relaxation times of freeze-dried lactose/whey protein isolate (WPI) systems were studied using dynamic dewpoint isotherms (DDI) method and dielectric analysis (DEA), respectively. The fractional water sorption behavior of lactose/WPI mixtures shown at aw ≤ 0.44 and the critical aw for water sorption-related crystallization (aw(cr)) of lactose were strongly affected by protein content based on DDI data. DEA results showed that the α-relaxation temperatures of amorphous lactose at various relaxation times were affected by the presence of water and WPI. The α-relaxation-derived strength parameter (S) of amorphous lactose decreased with aw up to 0.44 aw but the presence of WPI increased S. The linear relationship for aw(cr) and S for lactose/WPI mixtures was also established with R2 > 0.98. Therefore, DDI offers another structural investigation of water sorption-related crystallization as governed by aw(cr), and S may be used to describe real time effects of structural relaxations in noncrystalline multicomponent solids.

Optimal control of non-linear systems through hybrid cell-mapping/artificial-neural-networks techniques

In this paper, a real-time optimal control technique for non-linear plants is proposed. The control system makes use of the cell-mapping (CM) techniques, widely used for the global analysis of highly non-linear systems. The CM framework is employed for designing approximate optimal controllers via a control variable discretization. Furthermore, CM-based designs can be improved by the use of supervised feedforward artificial neural networks (ANNs), which have proved to be universal and efficient tools for function approximation, providing also very fast responses. The quantitative nature of the approximate CM solutions fits very well with ANNs characteristics. Here, we propose several control architectures which combine, in a different manner, supervised neural networks and CM control algorithms. On the one hand, different CM control laws computed for various target objectives can be employed for training a neural network, explicitly including the target information in the input vectors. This way, tracking problems, in addition to regulation ones, can be addressed in a fast and unified manner, obtaining smooth, averaged and global feedback control laws. On the other hand, adjoining CM and ANNs are also combined into a hybrid architecture to address problems where accuracy and real-time response are critical. Finally, some optimal control problems are solved with the proposed CM, neural and hybrid techniques, illustrating their good performance.

Investigating the Roles and Requirements, Manifestations and Management of Metadata in the Creation of Reliable and Preservation of Authentic Electronic Entities Created by Dynamic, Interactive and Experiential Systems: Report on the Work and Findings of the Interpares 2 Description Cross Domain Group

Metadata that is associated with either an information system or an information object for purposes of description, administration, legal requirements, technical functionality, use and usage, and preservation, plays a critical role in ensuring the creation, management, preservation and use and re-use of trustworthymaterials, including records. Recordkeeping1 metadata, of which one key type is archival description, plays a particularly important role in documenting the reliability and authenticity of records and recordkeeping systemsas well as the various contexts (legal-administrative, provenancial, procedural, documentary, and technical) within which records are created and kept as they move across space and time. In the digital environment, metadata is also the means by which it is possible to identify how record components – those constituent aspects of a digital record that may be managed, stored and used separately by the creator or the preserver – can be reassembled to generate an authentic copy of a record or reformulated per a user’s request as a customized output package.Issues relating to the creation, capture, management and preservation of adequate metadata are, therefore, integral to any research study addressing the reliability and authenticity of digital entities, regardless of the community, sector or institution within which they are being created. The InterPARES 2 Description Cross-Domain Group (DCD) examined the conceptualization, definitions, roles, and current functionality of metadata and archival description in terms of requirements generated by InterPARES 12. Because of the needs to communicate the work of InterPARES in a meaningful way across not only other disciplines, but also different archival traditions; to interface with, evaluate and inform existing standards, practices and other research projects; and to ensure interoperability across the three focus areas of InterPARES2, the Description Cross-Domain also addressed its research goals with reference to wider thinking about and developments in recordkeeping and metadata. InterPARES2 addressed not only records, however, but a range of digital information objects (referred to as “entities” by InterPARES 2, but not to be confused with the term “entities” as used in metadata and database applications) that are the products and by-products of government, scientific and artistic activities that are carried out using dynamic, interactive or experiential digital systems. The nature of these entities was determined through a diplomatic analysis undertaken as part of extensive case studies of digital systems that were conducted by the InterPARES 2 Focus Groups. This diplomatic analysis established whether the entities identified during the case studies were records, non-records that nevertheless raised important concerns relating to reliability and authenticity, or “potential records.” To be determined to be records, the entities had to meet the criteria outlined by archival theory – they had to have a fixed documentary format and stable content. It was not sufficient that they be considered to be or treated as records by the creator. “Potential records” is a new construct that indicates that a digital system has the potential to create records upon demand, but does not actually fix and set aside records in the normal course of business. The work of the Description Cross-Domain Group, therefore, addresses the metadata needs for all three categories of entities.Finally, since “metadata” as a term is used today so ubiquitously and in so many different ways by different communities, that it is in peril of losing any specificity, part of the work of the DCD sought to name and type categories of metadata. It also addressed incentives for creators to generate appropriate metadata, as well as issues associated with the retention, maintenance and eventual disposition of the metadata that aggregates around digital entities over time.