Προσομοιωτής κβαντικών κυκλωμάτων στο αναπτυξιακό περιβάλλον παράλληλης επεξεργασίας CUDA

Οι κβαντικοί υπολογιστές είναι μια ερευνητική περιοχή με αυξανόμενο ενδιαφέρον. Η ιδέα τους είναι θεμελιωδώς διαφορετική από τους κλασικούς ψηφιακούς υπολογιστές και για τον λόγο αυτό απαιτούν νέες τεχνολογίες κατασκευής, νέους τρόπους σχεδιασμού και νέους αλγόριθμους. Η υπάρχουσα υποδομή κβαντικών υπολογιστών είναι μηδαμινή, πράγμα που δυσκολεύει την έρευνα αφού δεν υπάρχουν πραγματικά συστήματα μεγάλης κλίμακας για την υλοποίηση και τον έλεγχο της θεωρίας και των ιδεών. Αυτή η εργασία έχει σκοπό να βοηθήσει στην επίλυση αυτού του προβλήματος με την δημιουργία ενός προσομοιωτή κβαντικών κυκλωμάτων πάνω στα οποία θα δοκιμάζονται κβαντικοί αλγόριθμοι. Το εργαλείο αυτό θα είναι εύκολα προσβάσιμο και δεν θα απαιτεί πολλούς πόρους για την εκτέλεση του. Θα προσομοιώνει δίνοντας έμφαση στην καλύτερη απόδοση από άποψη χρόνου εκτέλεσης και από άποψη δυνατότητας να λειτουργεί για μεγάλο αριθμού qubits. Για να επιτευχθεί ο σκοπός αποφασίστηκε να γίνει χρήση καρτών γραφικών (GPU), οι αρχιτεκτονικές των οποίων επιτρέπουν την μαζικά παράλληλη εκτέλεση των πράξεων που απαιτεί η προσομοίωση κβαντικών υπολογιστών με κλασικούς υπολογιστές. Συγκεκριμένα επιλέχθηκε η πλατφόρμα ανάπτυξης CUDA της NVidia που πρόκειται για δημοφιλή και διαδεδομένη επιλογή, και οι κάρτες της υπάρχουν σε πολυάριθμα εργαστήρια. To πρώτο βήμα της εργασίας, ήταν η μελέτη της απαιτούμενης θεωρίας. Αυτό περιλαμβάνει την κατανόηση των θεμελιωδών κβαντικών στοιχείων, των κβαντικών πυλών, των κβαντικών υπολογισμών και πως αυτοί υλοποιούνται. Από άποψη των GPU, περιλαμβάνει τις υπάρχουσες αρχιτεκτονικές, τα χαρακτηριστικά τους, πως υλοποιούν τους παράλληλους υπολογισμούς και πως γίνεται σωστή χρήση για εκμετάλλευση των δυνατοτήτων τους στο έπακρο. Μετά την κατανόηση της θεωρίας, ακολούθησε η θεωρητική σχεδίαση του αλγορίθμου που θα εκτελεί τους υπολογισμούς. Ακόμα, σχεδιάστηκε η μορφή που θα έχει η είσοδος του χρήστη στο εργαλείο, πως τα δεδομένα θα διαβάζονται, θα αποθηκεύονται και θα επεξεργάζονται. Στην συνέχεια έγινε η ανάπτυξη του κώδικα με προσοχή στην τήρηση των παραπάνω. Από κει και πέρα ξεκίνησε πρακτική δοκιμή του κώδικα σε πραγματικές κάρτες, ώστε να γίνουν φανερά τα αποτελέσματα της θεωρητικής σχεδίασης και να ακολουθήσει βελτίωση με πρακτική εφαρμογή. Υλοποιήθηκαν γνωστοί κβαντικοί αλγόριθμοι και κυκλώματα και πάρθηκαν μετρήσεις για την απόδοσή τους με χρήση ειδικών εργαλείων. Η λειτουργία του προσομοιωτή με λίγα λόγια είναι η εξής. Ο χρήστης εισάγει ένα αρχείο κειμένου το οποίο περιέχει το κύκλωμα προς εκτέλεση γραμμένο με μια γλώσσα περιγραφής που σχεδιάστηκε γι’ αυτό το σκοπό. Γίνεται ανάλυση του κειμένου, μεταφέρονται δεδομένα στην κάρτα γραφικών και εκτελούνται οι απαραίτητες πράξεις. Όταν ολοκληρωθούν όλοι οι υπολογισμοί, επιστρέφουν τα αποτελέσματα από την κάρτα και γίνεται καταγραφή τους σε αρχεία κειμένου ώστε να μπορούν να διαβαστούν από τον χρήστη.Quantum computers is a research field of study with increasing interest. The idea behind them is fundamentally different from the classical digital computers and for that reason they require new manufacturing technologies, new design methods and new algorithms. The existing infrastructure of quantum computers is minimal, and makes the research difficult due to the lack of large scale real systems for implementation and testing of theory and ideas. The purpose of this master's thesis is to help in the search for a solution to this problem with the creation of a quantum circuit simulator on which they can be tested quantum algorithms. This tool will be easily accessible and it will not require a lot of resources for its execution. It will simulate emphasizing on better performance in terms of execution time and in terms of the ability of performing on a large number of qubits. To achieve this purpose it was decided to use graphics cards (GPU), the architectures of which allow the massive parallel execution of operations, a fact that serves the enormous amount of operations that quantum computations require. Specifically the NVidia CUDA development platform was chosen because it is popular and widely used option, and the there are numerous laboratories with that type of cards. The first step of this project was the study of the required theory. This includes the understanding of the fundamental quantum elements, the quantum gates, the quantum calculations and how they are implemented. In terms of the GPU, it includes the existing architectures, their characteristics, how they implement parallel computations and how to be properly used to exploit their potential to the fullest. After understanding the theory, the next step was to design the theoretical algorithm that performs the calculations. In addition, the form of the user’s input to the tool was designed, how the data will be read, stored and processed. Then, the real code was developed with attention to the compliance of the above. After that, the testing of the code started on real cards, so to become apparent the results of the theoretical design and to improve the code by practice. Some known quantum algorithms and circuits were implemented and their performance was analyzed by using special tools. The operation of the simulator in short, is the following. The user enters a text file which contains the circuit written in a description language designed for this purpose. The tool analyses the text, sends the data to the card and the necessary operations are executed. When all the calculations are completed, the results return from the card and they are written in text files in order the user can read them

Characterization and Weathering of the Building Materials of Sanctuaries in the Archaeological Site of Dion, Greece

The sanctuaries of Demeter and Asklepios are part of the Dion archaeological site that sits among the eastern foothills of Mount Olympus. The main building materials are limestones and conglomerates. Sandstones, marbles, and ceramic plinths were also used. The materials consist mainly of calcite and/or dolomite, whereas the deteriorated surfaces contain also secondary and recrystallized calcite and dolomite, gypsum, various inorganic compounds, fluoroapatite, microorganisms and other organic compounds. Cracks and holes were observed in various parts of the stones. The influence of specific weathering agents and factors to the behavior of the materials was examined. The particular environmental conditions in Dion combine increased moisture and rain fall, insolation and great temperature differences, abundance of intensive surface and underground water bodies in the surrounding area, an area full of plants and trees, therefore, they can cause extensive chemical, biological and mechanical decay of the monuments. The following physical characteristics of the building materials have been studied: bulk density, open porosity, pore size distribution, water absorption and desorption, capillary absorption and desorption. The chemical composition of bulk precipitation, surface and underground water was investigated. The salts presence and crystallization was examined. The influence of the water presence to the behavior of the materials was examined by in situ IR thermometer measurements. Temperature values increased from the lower to the upper parts of the building stones and they significantly depend on the orientation of the walls. The results indicate the existence of water in the bulk of the materials due to capillary penetration. The existence of water in the bulk of the materials due to capillary penetration, the cycles of wet-dry conditions, correlated with the intensive surface and underground water presence in the whole surrounding area, lead to partial dissolution-recrystallization of the carbonate material and loss of the structural cohesion and the surface stability

LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome.

Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR's divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms

45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus

Research ArticleThe genus Avena comprises four distinct genomes organized in diploid (AA or CC), tetraploid (AABB or AACC) and hexaploid species (AACCDD), constituting an interesting model for phylogenetic analysis. The aim of this work was to characterize 45S rDNA intergenic spacer (IGS) variability in distinct species representative of Avena genome diversity±A. strigosa (AA), A. ventricosa (CvCv), A. eriantha (CpCp), A. barbata (AABB), A. murphyi (AACC), A. sativa (AACCDD) and A. sterilis (AACCDD) through the assessment of the 5' external transcribed spacer (5'-ETS), a promising IGS region for phylogenetic studies poorly studied in Avena genus. In this work, IGS length polymorphisms were detected mainly due to distinct 5'-ETS sequence types resulting from major differences in the number and organization of repeated motifs. Although species with A genome revealed a 5'-ETS organization (A-organization) similar to the one previously described in A. sativa, a distinct organization was unraveled in C genome diploid species (C-organization). Interestingly, such new organization presents a higher similarity with other Poaceae species than A-genome sequences, supporting the hypothesis of C-genome being the ancestral Avena genome. Additionally, polyploid species with both genomes mainly retain the A-genome 5'-ETS organization, confirming the preferential elimination of C-genome sequences in Avena polyploid species. Moreover, 5'-ETS sequences phylogenetic analysis consistently clustered the species studied according to ploidy and genomic constitution supporting the use of ribosomal genes to highlight Avena species evolutive pathways.info:eu-repo/semantics/publishedVersio