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The regular transmittance of light or similar radiation through a flowing suspension of particles fluctuates because of the random occurrence of particles in the beam.In the work presented here, a theory for this fluctuating behaviour with the emphasison dispersions of mm-length slender cylindrical particles having circular crosssections is given. The particles in question are wood pulp fibres, which as a first approximation are considered to have a cylinder shape. Four possible measurementprinciples are described theoretically and experimentally. The four principles are for the measurement of concentration, length distribution characterized as lengthclasses, mean length, and mean width. The usefulness in industrial process monitoring of two of these principles is exemplified with pulp measurements. In order to estimate model errors, numerical simulations were used. Although other techniques such as image analysis may compete, the technique presented here is attractive because of the simplicity of the measurement device used. / QC 20100806

Massively parallel whole transcriptome sequencing and its ability to generate full transcriptome data at the single transcript level provides a powerful tool with multiple interrelated applications, including transcriptome reconstruction, gene/isoform expression estimation, also known as transcriptome quantification. As a result, whole transcriptome sequencing has become the technology of choice for performing transcriptome analysis, rapidly replacing array-based technologies. The most commonly used transcriptome sequencing protocol, referred to as RNA-Seq, generates short (single or paired) sequencing tags from the ends of randomly generated cDNA fragments. RNA-Seq protocol reduces the sequencing cost and significantly increases data throughput, but is computationally challenging to reconstruct full-length transcripts and accurately estimate their abundances across all cell types. We focus on two main problems in transcriptome data analysis, namely, transcriptome reconstruction and quantification. Transcriptome reconstruction, also referred to as novel isoform discovery, is the problem of reconstructing the transcript sequences from the sequencing data. Reconstruction can be done de novo or it can be assisted by existing genome and transcriptome annotations. Transcriptome quantification refers to the problem of estimating the expression level of each transcript. We present a genome-guided and annotation-guided transcriptome reconstruction methods as well as methods for transcript and gene expression level estimation. Empirical results on both synthetic and real RNA-seq datasets show that the proposed methods improve transcriptome quantification and reconstruction accuracy compared to previous methods.

In this work, the material distribution, structure of fiber orientation and fiber attrition in sandwich and push-pull injection molded short fiber composites are investigated, regarding the effect of fiber content and processing parameters, given its direct relevance to mechanical properties. The prediction of the tensile strength of conventional, sandwich and push-pull injection molded short fiber composites are derived by an analytical method of modified rule of mixtures as a function of the area fraction between skin and core layers. The effects of fiber length and fiber orientation on the tensile strength are studied in detail. Modeling of the specialized injection molding processes have been developed and performed with the simulation program in order to predict the material distribution and the fiber orientation state. The secondorder orientation tensor (a11) approach is used to describe and calculate the local fiber orientation state. The accuracy of the model prediction is verified by comparing with corresponding experimental measurements to gain a further basic understanding of the melt flow induced fiber orientation during sandwich and push-pull injection molding processes.

Η μικρή παράκτια αλιεία αποτελεί σημαντικό τμήμα του αλιευτικού κλάδου στnν Ελλάδα και τη Μεσόγειο και χαρακτηρίζεται από υψηλή ετερογένεια και πληθώρα ιδιαιτεροτήτων. Η διαχείριση της απαιτεί την εξέταση βιολογικών, αλλά και κοινωνικών και οικονομικών παραμέτρων. Στην παρούσα εργασία αναπτύχθηκε μία τυπολογία της ελληνικής μικρής παράκτιας αλιείας με βάση βιολογικά, κοινωνικά και οικονομικά χαρακτηριστικά. Στη συνέχεια η εργασία εστιάστηκε στον Πατραϊκό Κόλπο, όπου μελετήθηκε η δραστηριότητα της τοπικής μικρής παράκτιας αλιείας, η συνολική παραγωγή και η παραγωγή ανά μονάδα αλιευτικής προσπάθειας, η σύνθεση του αλιεύματος, τα απορριπτόμενα και η κατά μήκος σύνθεση των αλιευμάτων. Οι νομοί της Ελλάδας στρωματοποιήθηκαν βάσει του αριθμού των αλιέων και της εξάρτησης από την αλιεία και πραγματοποιήθηκαν συνεντεύξεις αλιέων. Επιβεβαιώθηκε η ποικιλία εργαλείων και ειδών-στόχων και η έντονη χωρική ετερογένεια. Το κυρίαρχο πρότυπο αλιευτικής δραστηριότητας εμφάνισε εποχικές διακυμάνσεις (20 ημέρες δραστηριότητας μηνιαίως το καλοκαίρι, 13 ημέρες το χειμώνα), παρουσίασε όμως τοπικές ιδιαιτερότητες. Οι κύριες ενασχολήσεις (métiers) που πραγματοποιούνται σε πανελλήνιο επίπεδο αναγνωρίστηκαν ως συνδυασμοί αλιευτικού εργαλείου, είδους-στόχου, εποχής και περιοχής με πολυμεταβλητή ανάλυση. Οι αλιείς παρουσίασαν χαμηλό μορφωτικό επίπεδο και υψηλή μέση ηλικία, υψηλά ποσοστά παραμονής στον τόπο γέννησης και διαπιστώθηκε έντονη παρουσία της οικογένειας στο επάγγελμα. Οι αλιείς χωρίστηκαν σε τρεις ομάδες εξάρτησης από την αλιεία βάσει του ποσοστού του εισοδήματος που προέρχεται από το ψάρεμα, οι οποίες εμφάνισαν διαφορές σε χαρακτηριστικά όπως η μέση ηλικία, το μήκος του σκάφους, οι ημέρες δραστηριότητας και το εισόδημα από το ψάρεμα. Στη συνέχεια μελετήθηκε η μικρή παράκτια αλιεία του Πατραϊκού Κόλπου με δειγματοληψίες σε αλιευτικές εξορμήσεις. Η αλιευτική παραγωγή ήταν κατά μέσο όρο 12 Kg ανά αλιευτική εξόρμηση. Συνολικά, αναγνωρίστηκαν 102 είδη αλιευμάτων. Αναπτύχθηκε μία μεθοδολογία αναγνώρισης ενασχολήσεων σε περιπτώσεις περιορισμένου αριθμού δεδομένων, όπως συχνά συμβαίνει στη Μεσόγειο. Οι ενασχολήσεις που αναγνωρίστηκαν παρουσίασαν διαφορές στην ποσότητα και στη σύνθεση του αλιεύματος και ομαδοποιήθηκαν σε μετα-ενασχολήσεις με σκοπό την αποτελεσματικότερη δειγματοληψία της αλιευτικής δραστηριότητας. Η μελέτη των απορριπτομένων ανέδειξε τρεις αιτίες απόρριψης: χαμηλή εμπορικότητα (78% της απορριφθείσας ποσότητας), καταστροφή των αλιευμάτων κατά την παραμονή τους στο νερό (5%) και μείωση της ποιότητάς τους εξαιτίας κακών χειρισμών του ψαρά (17%). Υψηλό ποσοστό απόρριψης παρουσίασαν οι ενασχολήσεις παραγαδιών και μανωμένων διχτύων με μικρό άνοιγμα ματιού. Από τα δεδομένα ατομικού μήκους των αλιευμάτων πραγματοποιήθηκαν συγκρίσεις κατά μήκους σύνθεσης ανάμεσα σε διαφορετικές ενασχολήσεις και εποχές του έτους. Στις περισσότερες περιπτώσεις διαπιστώθηκαν διαφορές. Η μελέτη της επίπτωσης της εφαρμογής του ελάχιστου επιτρεπόμενου μεγέθους εκφόρτωσης έδειξε μικρό ποσοστό υπομεγεθών ατόμων στο αλίευμα βάσει τόσο των σημερινών σε ισχύ μεγεθών όσο και βάσει αυτών που πρόκειται να εφαρμοστούν σύμφωνα με τον Οδικό Χάρτη για την Αναθεώρηση της Κοινής Αλιευτικής Πολιτικής, σε επίπεδο είδους όμως παρουσιάστηκαν εξαιρέσεις. Η παρούσα εργασία αποτελεί τη βάση για την ανάπτυξη μεθοδολογίας για τη μελέτη της μικρής παράκτιας αλιείας στην Ελλάδα και την πραγματοποίηση συγκριτικών μελετών σε ευρωπαϊκή κλίμακα σε αυτόν τον λίγο μελετημένο αλιευτικό κλάδο. / Small-scale fisheries are an important fisheries sector in Greece and the Mediterranean. They are characterized by high heterogeneity and a multitude of particularities. The management of small-scale fisheries requires taking into account biological as well as social and economical elements. In the present study, a typology of Greek small-scale fisheries was developed based on biological, social and economical parameters. Consequently, the study focused in the Patraikos Gulf, where elements such as the fishing activity of the local fleet, catch and catch per unit of effort, species composition, discards and length composition of individuals caught were examined. The prefectures of Greece were stratified considering the number of fishermen and local dependence on fisheries and interviews of fishermen were carried out. The multitude of fishing gears and target species and the intense spatial heterogeneity was confirmed. The major activity pattern identified was seasonal (20 days of activity in summer, 13 in winter), however local particularities arose. The main métiers practiced were identified as combinations of fishing gear, target species, area and season. Concerning socio-economical elements, the fishermen generally had low education, high average age, tendency to remain in their place of birth and the profession is attached to the family. The fishermen were categorized into three dependence groups, based on the percentage of income originating from fisheries. Significant differences were identified among these groups considering variables such as mean fishermen age, vessel size, days of activity and income from fishing. Consequently, the small-scale fisheries of the Patraikos Gulf were studied using data from sampling of fishing operations. The catch weighted about 12 Kg per operation on average and a total of 102 species were recorded. A methodology for the identification of métiers using a limited dataset, as is often the case in the Mediterranean, was developed. The métiers identified showed significant differences in catch quantity and composition and were grouped in meta-métiers to facilitate fishing activity sampling schemes. The study of discards revealed three reasons for discarding: low commercial value (78% of discards), destruction of the catch before gear retrieval (5%) and bad handling of the catch o board (17%). High discard ratio was recorded for the longline and small-size mesh trammel net métiers. Using data of individual length per species comparisons were carried out among métiers and seasons that in most cases revealed significant differences. The study of the effect of minimum landing sizes legislation showed a low percentage of undersized individuals regarding both the legislation currently in effect and the proposed one by the Roadmap for the Reform of the Common Fisheries Policy of the European Union, but exceptions arose for certain species. The present work is the foothold for the development of a methodology for studying small-scale fisheries in Greece and for carrying out comparative studies in a European scale concerning this understudied fishing sector.

An investigation into the impact of generalised maximum entropy solutions on the study of queues with or without arrival balking and their applications to congestion management in communication networks Keywords: Queues, Balking, Maximum Entropy (ME) Principle, Global Balance (GB), Queue Length Distribution (QLD), Generalised Geometric (GGeo), Generalised Exponential (GE), Generalised Discrete Half Normal (GdHN), Congestion Management, Packet Dropping Policy (PDP) Generalisations to links between discrete least biased (i.e. maximum entropy (ME)) distribution inferences and Markov chains are conjectured towards the performance modelling, analysis and prediction of general, single server queues with or without arrival balking. New ME solutions, namely the generalised discrete Half Normal (GdHN) and truncated GdHN (GdHNT) distributions are characterised, subject to appropriate mean value constraints, for inferences of stationary discrete state probability distributions. Moreover, a closed form global balance (GB) solution is derived for the queue length distribution (QLD) of the M/GE/1/K queue subject to extended Morse balking, characterised by a Poisson prospective arrival process, i.i.d. generalised exponential (GE) service times and finite capacity, K. In this context, based on comprehensive numerical experimentation, the latter GB solution is conjectured to be a special case of the GdHNT ME distribution. ii Owing to the appropriate operational properties of the M/GE/1/K queue subject to extended Morse balking, this queueing system is applied as an ME performance model of Internet Protocol (IP)-based communication network nodes featuring static or dynamic packet dropping congestion management schemes. A performance evaluation study in terms of the model’s delay is carried out. Subsequently, the QLD’s of the GE/GE/1/K censored queue subject to extended Morse balking under three different composite batch balking and batch blocking policies are solved via the technique of GB. Following comprehensive numerical experimentation, the latter QLD’s are also conjectured to be special cases of the GdHNT. Limitations of this work and open problems which have arisen are included after the conclusions.

Cette thèse consiste en trois parties que j'ai faites pendant ces trois ans.La première partie va être constituée de l'étude de la distribution de la longueur de corde sur le plan hyperbolique. Nous montrons l'identité de Pleijel pour le plan hyperbolique. En utilisant cette identité, nous remontrons l'identité de formule de Crofton et l'inégalité isopérimétrique pour le plan hyperbolique, et puis nous calculons la distribution de la longueur de corde associée à un triangle idéal et celle associée à un quadrilatère idéal. Ensuit, nous montons les résultats analogues pour les surfaces riemannienne simplement connexes avec la courbure constante. La seconde partie va contribuer aux études de la métrique de pression sur l'espace de Teichmüller d'un tore privé d'un disque. En étudiant la dégénération du tore quand la longueur du bord va à l'infini, nous trouvons la relation de cette métrique avec la métrique de pression sur l'espace modulaires des graphes métriques. Nous montrons ensuite que la fonction de l'entropie n'est pas constante sur les feuilles symplectique de l'espace Teichmüller d'une surface à bord.Finalement, la troisième partie concerne la quantification de l'espace de Teichmüller d'une surface avec les piqûres. nous montrons. Dans ce chapitre, nous étudions l'extension centrale du groupe modulaire via la quantification de Chekhov-Fock et calculons sa classe de cohomologie qui est 12 fois la classe de Meyer plus les classes d'Euler associées aux piqûres. / This thesis consists of three parts corresponding to the three subjects that I have studied during the last three years.The first part contains the study of the chord length distribution associated to a compact (or non-compact) domain in the hyperbolic plane. We prove the hyperbolic Pleijel identity. By using this identity, we find new approaches to the Crofton's formula and the isoperimetric inequality, and then compute the chord length distribution associated to an ideal triangle and that associated to an ideal quadrilateral. Then we prove the analogue results for the simply connected Riemannian surface with constant curvature.The second part of this thesis (Chapter 5) consists of the study of the pressuremetric on the Teichmüller space of one-holed torus. By studying the degeneration of the torus when the boundary length goes to infinity, we find the relation of this metric to the pressure metric on the moduli space of metric graphs. Then we study the entropy function and prove that it is not constant on the symplectic leaf of the Teichmüller space of a bordered surface.Finally, the third part concerns the quantization of the Teichmüller space of a punctured surface. In this chapter, we study the central extension of the mapping class group coming from the quantization and compute its cohomology class which is 12 times the Meyer class plus the Euler classes associated to punctures.

In this work, the material distribution, structure of fiber orientation and fiber attrition in sandwich and push-pull injection molded short fiber composites are investigated, regarding the effect of fiber content and processing parameters, given its direct relevance to mechanical properties. The prediction of the tensile strength of conventional, sandwich and push-pull injection molded short fiber composites are derived by an analytical method of modified rule of mixtures as a function of the area fraction between skin and core layers. The effects of fiber length and fiber orientation on the tensile strength are studied in detail. Modeling of the specialized injection molding processes have been developed and performed with the simulation program in order to predict the material distribution and the fiber orientation state. The secondorder orientation tensor (a11) approach is used to describe and calculate the local fiber orientation state. The accuracy of the model prediction is verified by comparing with corresponding experimental measurements to gain a further basic understanding of the melt flow induced fiber orientation during sandwich and push-pull injection molding processes.

An investigation into the impact of generalised maximum entropy solutions on the study of queues with or without arrival balking and their applications to congestion management in communication networks Keywords: Queues, Balking, Maximum Entropy (ME) Principle, Global Balance (GB), Queue Length Distribution (QLD), Generalised Geometric (GGeo), Generalised Exponential (GE), Generalised Discrete Half Normal (GdHN), Congestion Management, Packet Dropping Policy (PDP) Generalisations to links between discrete least biased (i.e. maximum entropy (ME)) distribution inferences and Markov chains are conjectured towards the performance modelling, analysis and prediction of general, single server queues with or without arrival balking. New ME solutions, namely the generalised discrete Half Normal (GdHN) and truncated GdHN (GdHNT) distributions are characterised, subject to appropriate mean value constraints, for inferences of stationary discrete state probability distributions. Moreover, a closed form global balance (GB) solution is derived for the queue length distribution (QLD) of the M/GE/1/K queue subject to extended Morse balking, characterised by a Poisson prospective arrival process, i.i.d. generalised exponential (GE) service times and finite capacity, K. In this context, based on comprehensive numerical experimentation, the latter GB solution is conjectured to be a special case of the GdHNT ME distribution. ii Owing to the appropriate operational properties of the M/GE/1/K queue subject to extended Morse balking, this queueing system is applied as an ME performance model of Internet Protocol (IP)-based communication network nodes featuring static or dynamic packet dropping congestion management schemes. A performance evaluation study in terms of the model’s delay is carried out. Subsequently, the QLD’s of the GE/GE/1/K censored queue subject to extended Morse balking under three different composite batch balking and batch blocking policies are solved via the technique of GB. Following comprehensive numerical experimentation, the latter QLD’s are also conjectured to be special cases of the GdHNT. Limitations of this work and open problems which have arisen are included after the conclusions

Controlled radical polymerization (CRP) can be viewed as the middle ground between living anionic polymerization (LAP) and conventional free radical polymerization (FRP). It combines the precise control over polymer structure offered by LAP, under a tolerant reaction condition similar to FRP. One of the most studied CRP is atom transfer radical polymerization (ATRP), with over 10,000 papers published since its introduction in 1995. Despite the numerous studies, knowledge on its fundamental mechanism is still lacking, as evident from the lack of expression for full MWD and polydispersity that account for termination reaction. Since termination is unavoidable in ATRP, the existing expressions give inaccurate predictions as dead chains accumulate. In this study, we derived expressions for full MWD at low conversion and for polydispersity. These expressions allow us to quantify and gain better understanding on the contribution of termination. In addition, the resulting polydispersity expression shows better agreement than the existing equation when correlated with experiment data. In addition to the aforementioned questions, there are also controversies regarding the kinetics of surface-initiated ATRP, with researchers divided into two schools of theories. We evaluated the validity of these theories by comparing their predictions to experimental trends. Both theories were found to be inadequate in explaining all the experimental observations, thus triggering an investigation of the graft density. Graft density is an important determining property for polymer brushes, yet little is known about what affects its final value. Through simulations, we investigated the effect of experiment factors on the grafting density. A decrease in the amount of deactivator is found to decrease the grafting density, which could be explained by an increase in the number of monomers added per activation cycle. This knowledge allows us to explain the conflicting experiment observations regarding the growth trends of polymer layers reported in the literatures. / Thesis / Doctor of Philosophy (PhD) / Polymer materials are used almost everywhere in our daily life from clothing to water bottle. This wide range of applications owes to the nearly infinite possible properties that polymer can possess. Different polymerization processes to synthesize polymers have their own weaknesses and strengths. Herein we investigated the fundamental mechanism of one of the currently most attractive polymerization systems, atom transfer radical polymerization (ATRP). This process allows the synthesis of polymers with precisely tailored chain microstructures, making it possible to create polymer with sophisticated properties. Using modeling approaches, we derived explicit expressions for determining chain properties, allowing detailed investigation of how various factors affect these properties. Through these investigations, we obtained better understanding on the mechanism of ATRP in solution and on surface. This knowledge is crucial in providing insight and guiding experimental designs for better control over the material properties.