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319 results on '"Dimitrakis, P."'

1. Quantum gate algorithm for reference-guided DNA sequence alignment

Author

Varsamis, G. D., Karafyllidis, I. G., Gilkes, K. M., Arranz, U., Martin-Cuevas, R., Calleja, G., Dimitrakis, P., Kolovos, P., Sandaltzopoulos, R., Jessen, H. C., and Wong, J.

Subjects
Quantitative Biology - Biomolecules, Quantum Physics
Abstract

Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be re-sequenced. Each human genome has 3.2 B base pairs, and each one could be stored with 2 bits of information, so one human genome would take 6.4 B bits or about 760 MB of storage (National Institute of General Medical Sciences). Today most powerful tensor processing units cannot handle the volume of DNA data necessitating a major leap in computing power. It is, therefore, important to investigate the usefulness of quantum computers in genomic data analysis, especially in DNA sequence alignment. Quantum computers are expected to be involved in DNA sequencing, initially as parts of classical systems, acting as quantum accelerators. The number of available qubits is increasing annually, and future quantum computers could conduct DNA sequencing, taking the place of classical computing systems. We present a novel quantum algorithm for reference-guided DNA sequence alignment modeled with gate-based quantum computing. The algorithm is scalable, can be integrated into existing classical DNA sequencing systems and is intentionally structured to limit computational errors. The quantum algorithm has been tested using the quantum processing units and simulators provided by IBM Quantum, and its correctness has been confirmed., Comment: 19 pages, 13 figures

Published
2023
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2. Quantum algorithm for de novo DNA sequence assembly based on quantum walks on graphs

Author

Varsamis, G. D., Karafyllidis, I. G., Gilkes, K. M., Arranz, U., Martin-Cuevas, R., Calleja, G., Wong, J., Jessen, H. C., Dimitrakis, P., Kolovos, P., and Sandaltzopoulos, R.

Subjects
Quantitative Biology - Biomolecules, Quantum Physics
Abstract

De novo DNA sequence assembly is based on finding paths in overlap graphs, which is a NP-hard problem. We developed a quantum algorithm for de novo assembly based on quantum walks in graphs. The overlap graph is partitioned repeatedly to smaller graphs that form a hierarchical structure. We use quantum walks to find paths in low rank graphs and a quantum algorithm that finds Hamiltonian paths in high hierarchical rank. We tested the partitioning quantum algorithm, as well as the quantum algorithm that finds Hamiltonian paths in high hierarchical rank and confirmed its correct operation using Qiskit. We developed a custom simulation for quantum walks to search for paths in low rank graphs. The approach described in this paper may serve as a basis for the development of efficient quantum algorithms that solve the de novo DNA assembly problem., Comment: 13 pages, 7 figures

Published
2023

4. Multi-level resistance switching and random telegraph noise analysis of nitride based memristors

Author

Vasileiadis, Nikolaos, Loukas, Panagiotis, Karakolis, Panagiotis, Ioannou-Sougleridis, Vassilios, Normand, Pascal, Ntinas, Vasileios, Fyrigos, Iosif-Angelos, Karafyllidis, Ioannis, Sirakoulis, Georgios Ch., and Dimitrakis, Panagiotis

Subjects
Physics - Applied Physics, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Resistance switching devices are of special importance because of their application in resistive memories (RRAM) which are promising candidates for replacing current nonvolatile memories and realize storage class memories. These devices exhibit usually memristive properties with many discrete resistance levels and implement artificial synapses. The last years, researchers have demonstrated memristive chips as accelerators in computing, following new in-memory and neuromorphic computational approaches. Many different metal oxides have been used as resistance switching materials in MIM or MIS structures. Understanding of the mechanism and the dynamics of resistance switching is very critical for the modeling and use of memristors in different applications. Here, we demonstrate the bipolar resistance switching of silicon nitride thin films using heavily doped Si and Cu as bottom and top-electrodes, respectively. Analysis of the current-voltage characteristics reveal that under space-charge limited conditions and appropriate current compliance setting, multi-level resistance operation can be achieved. Furthermore, a flexible tuning protocol for multi-level resistance switching was developed applying appropriate SET/RESET pulse sequences. Retention and random telegraph noise measurements performed at different resistance levels. The present results reveal the attractive properties of the examined devices.

Published
2021
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6. Versatile Filamentary Resistive Switching Model

Author

Fyrigos, Iosif-Angelos, Ntinas, Vasileios, Sirakoulis, Georgios Ch., Dimitrakis, Panagiotis, and Karafyllidis, Ioannis G.

Subjects
Computer Science - Emerging Technologies
Abstract

Memristors as emergent nano-electronic devices have been successfully fabricated and used in non-conventional and neuromorphic computing systems in the last years. Several behavioral or physical based models have been developed to explain their operation and to optimize their fabrication parameters. All existing memristor models are trade-offs between accuracy, universality and realism, but, to the best of our knowledge, none of them is purely characterized as quantum mechanical, despite the fact that quantum mechanical processes are a major part of the memristor operation. In this paper, we employ quantum mechanical methods to develop a complete and accurate filamentary model for the resistance variation during memristor's operating cycle. More specifically, we apply quantum walks to model and compute the motion of atoms forming the filament, tight-binding Hamiltonians to capture the filament structure and the Non-Equilibrium Green's Function (NEGF) method to compute the conductance of the device. Furthermore, we proceeded with the parallelization of the overall model through Graphical Processing Units (GPUs) to accelerate our computations and enhance the model's performance adequately. Our simulation results successfully reproduce the resistive switching characteristics of memristors devices, match with existing fabricated devices experimental data, prove the efficacy and robustness of the proposed model in terms of multi-parameterization, and provide a new and useful insight into its operation., Comment: 8 pages, 8 figures, submitted to IEEE Transactions on Nanotechnology (TNANO)

Published
2020

12. Experimental Evaluation of Silicon Nitride Memristors as Coupling Elements for Chimera States in Chaotic Oscillator Networks

Author

Tsakalos, Karolos-Alexandros, Ntinas, Vasileios, Vasileiadis, Nikolaos, Provata, Astero, Dimitrakis, Panagiotis, and Sirakoulis, Georgios Ch.

Abstract

Chimera states have attracted significant research interest due to their potential in modeling brain network functionality. Memristive nano-crossbars, known for their energy efficiency, massive parallelism, and synaptic-like properties, serve as a promising coupling medium in brain-inspired applications. The operation of these devices is strongly dictated by the non-linear mechanisms of memristor devices when studying synchronization phenomena. Expanding upon our previous work, which explored sneak-path currents in Chimera states, this study investigates the impact of fabricated Silicon Nitride (SiN) devices on the dynamics of Chua circuit (CC) networks. We conducted experimental evaluations to confirm the ability of SiN devices to retain their resistance state, thereby ensuring consistency in the crossbar array, a critical factor in maintaining chimera states during experiments. We employed an exponential memristor model to further investigate the non-linear dynamics within the CC network. Our results not only confirm the formation of various synchronization structures, such as chimera states and full chaotic synchronization but also reveal the intriguing formation of phase-lag structures. These structures, induced by the SiN-fitted model, exhibit distinctive characteristics marked by subtle and non-linear coupling behaviors, particularly evident at near-zero voltages. After analyzing our results, we present a comprehensive phase-parametric regime map, obtained by varying the coupling strength bifurcation parameter. This map provides valuable insights into the mechanisms governing the dynamics of CC networks equipepd with SiN-based memristor nanodevices, which have proven capable of capturing the complex dynamics of chimera states.

Published
2025
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13. Nano-composite MOx materials for NVMs

Author

Bonafos, C., primary, Khomenkhova, L., additional, Gourbilleau, F., additional, Talbot, E., additional, Slaoui, A., additional, Carrada, M., additional, Schamm-Chardon, S., additional, Dimitrakis, P., additional, and Normand, P., additional

Published
2022
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14. Contributors

Author

Antonov, I.N., primary, Belov, A.I., additional, Bonafos, C., additional, Brivio, S., additional, Cario, Laurent, additional, Carrada, M., additional, Caussat, Brigitte, additional, Ch. Sirakoulis, Georgios, additional, Christensen, Dennis Valbjørn, additional, Cianci, Elena, additional, Corraze, Benoit, additional, Demin, V.A., additional, Dimitrakis, P., additional, Emelyanov, A.V., additional, Escudero, Manuel, additional, Esposito, Vincenzo, additional, Filatov, D.O., additional, Giannopoulos, Georgios, additional, Gorshkov, O.N., additional, Gourbilleau, F., additional, Gryaznov, E.G., additional, Guseinov, D.V., additional, Hoffmann, Michael, additional, Janod, Etienne, additional, Kaidatzis, Andreas, additional, Khomenkhova, L., additional, Korolev, D.S., additional, Koryazhkina, M.N., additional, Li, Yang, additional, Liu, Qi, additional, Max, Benjamin, additional, Mikhaylov, A.N., additional, Mikolajick, Thomas, additional, Mulaosmanovic, Halid, additional, Niarchos, Dimitris, additional, Nikiruy, K.E., additional, Normand, P., additional, Okulich, E.V., additional, Okulich, V.I., additional, Pavlov, D.A., additional, Pryds, Nini, additional, Ramkumar, Krishnaswamy, additional, Rubio, Antonio, additional, Rylkov, V.V., additional, Sanna, Simone, additional, Schamm-Chardon, S., additional, Schroeder, Uwe, additional, Shenina, M.E., additional, Shuisky, R.A., additional, Sidorenko, K.V., additional, Slaoui, A., additional, Slesazeck, Stefan, additional, Spagnolo, B., additional, Spiga, Sabina, additional, Talbot, E., additional, Tappertzhofen, Stefan, additional, Tetelbaum, D.I., additional, Tikhov, S.V., additional, Tranchant, Julien, additional, Vahlas, Constantin, additional, Vianello, E., additional, Vourkas, Ioannis, additional, and Zhao, Xiaolong, additional

Published
2022
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17. Quantum gate algorithm for reference-guided DNA sequence alignment

Author

Varsamis, G.D., primary, Karafyllidis, I.G., additional, Gilkes, K.M., additional, Arranz, U., additional, Martin-Cuevas, R., additional, Calleja, G., additional, Dimitrakis, P., additional, Kolovos, P., additional, Sandaltzopoulos, R., additional, Jessen, H.C., additional, and Wong, J., additional

Published
2023
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38. Nano-composite MOx materials for NVMs

Author

Bonafos, Caroline, Khomenkhova, L., Gourbilleau, F., Talbot, Etienne, Slaoui, Abdelilah, Carrada, Marzia, Schamm-Chardon, Sylvie, Dimitrakis, P., Normand, P., Centre d'élaboration de matériaux et d'études structurales (CEMES), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Matériaux, Défauts et IRradiations (MADIR), Centre de recherche sur les Ions, les MAtériaux et la Photonique (CIMAP - UMR 6252), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), V.E. Lashkaryov Institute of Semiconductor Physics, National Academy of Sciences of Ukraine (NASU), Groupe de physique des matériaux (GPM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institute of Nanoscience and Nanotechnology 'Demokritos' [Greece] (INN), National Center for Scientific Research 'Demokritos' (NCSR), ANR Project : ANR-PNAN-O07-0053-NOMAD, Talbot, Etienne, Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract

International audience; In this chapter, we will present a digest of the main materials science aspects of the controlled fabrication of 2D arrays of semiconducting (Si, Ge) nanocrystals (NCs) in metal oxide high-κ dielectric layers by using two promising techniques, namely magnetron-sputtering and Ultra Low Energy-Ion Beam Synthesis. In particular, the phase separation process as well as the problems related to humidity penetration or controlled oxidation processes are among the discussed topics. The different state-of-the-art tools for structural characterization will also be described. Finally, the associated electrical characterizations will be presented in order to evaluate the potential of such nanocomposite metal oxide layers for NC memory applications.

Published
2022
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47. Proton radiation effects on nanocrystal non-volatile memories

Author

Verrelli, E., Tsoukalas, D., Kokkoris, M., Vlastou, R., Dimitrakis, P., and Normand, P.

Subjects
Metal oxide semiconductors -- Usage, Transistors -- Analysis, Business, Electronics, Electronics and electrical industries
Abstract

We report on proton radiation effects on Si-nanocrystal (Si-NCs) MOS capacitors and nMOS transistors aiming at non-volatile memory applications. Irradiation experiments were conducted on NC MOS capacitors using protons of 1.5 MeV and 6.5 MeV and on NC nMOS transistors using protons of 1.5 MeV. The range of doses investigated was ~ 1 to ~ 100 Mrad(Si[O.sub.2]). A 2-D layer of Si NCs with ~ 3 nm mean diameter and [10.sup.12] [cm.sup.-2] surface density was successfully achieved by low-energy (1 keV) ion-beam-synthesis in thin Si[O.sub.2] layers. After irradiation, programmed capacitors are found to undergo bit flip while programmed transistors are not. Charge retention measurements at room temperature for the write and erase states of irradiated and non-irradiated samples reveal that a significant memory window exists at an extrapolated time of ten years even after an irradiation dose as high as 120 Mrad (Si[O.sub.2]). The flat-band decay rate of the erase state in NC MOS capacitors does not depend on the irradiation-dose while the opposite occurs for the write state which is found to be directly dependent on [D.sub.it] values after irradiation. These results clearly indicate that NC Non-Volatile Memories (NVM) are promising radiation tolerant devices. Index Terms--Data retention, nanocrystal memories, nonvolatile memory (NVM), proton radiation effects.

Published
2007

48. Poster: Electronic Structure, Lattice Dynamics, and Transport

Author

Richter, Christoph, primary, Boschker, Hans, additional, Dietsche, Werner, additional, Mannhart, Jochen, additional, Brasse, M., additional, Jany, R., additional, Heyn, Ch., additional, Mannhart, J., additional, Wilde, M. A., additional, Grundler, D., additional, Tada, Masahiro, additional, Miyauchi, Yohei, additional, Yoshiya, Masato, additional, Yasuda, Hideyuki, additional, Sagarna, Leyre, additional, Maegli, Alexandra, additional, Yoon, Songhak, additional, Populoh, Sascha, additional, Shkabko, Andrey, additional, Weidenkaff, Anke, additional, Karthäuser, Silvia, additional, Manheller, Marcel, additional, Waser, Rainer, additional, Blech, Kerstin, additional, Simon, Ulrich, additional, Pengpan, T., additional, Boonthummo, A., additional, Togo, Atsushi, additional, Chaput, Laurent, additional, Tanaka, Isao, additional, Ramírez, M. A, additional, Simões, A. Z, additional, Longo, E., additional, Varela, J. A, additional, Xu, Pengxiang, additional, Schena, Timo, additional, Bihlmayer, Gustav, additional, Blügel, Stefan, additional, Thatribud, A., additional, Tungsurat, T., additional, Tan, X. L., additional, Chen, P. F., additional, Wang, L. F., additional, Zhi, B. W., additional, Wu, W. B., additional, Nikolaev, A. V., additional, Michel, K. H., additional, Tsvyashchenko, A. V., additional, Velichkov, A. I., additional, Salamatin, A. V., additional, Fomicheva, L. N., additional, Ryasny, G. K., additional, Sorokin, A. A., additional, Kochetov, O. I., additional, Budzynski, M., additional, Prieto, P., additional, Gómez, M. E., additional, Puig, T., additional, Obradors, X., additional, Palau, A., additional, Llordés, A., additional, Coll, M., additional, Vlad, R., additional, Gazquez, J., additional, Arbiol, J., additional, Guzmán, R., additional, Pomar, A., additional, Sandiumenge, F., additional, Ricart, S., additional, Rouco, V., additional, Ye, S., additional, Deutscher, G., additional, Chataigner, D., additional, Varela, M., additional, Magen, C., additional, Vanacken, J., additional, Gutierrez, J., additional, Moshchalkov, V. V., additional, Broglia, Giulia, additional, Montorsi, Monia, additional, Larcher, Luca, additional, Padovani, Andrea, additional, Nasr Esfahani, D., additional, Covaci, L., additional, Peeters, F. M., additional, Ohnishi, Hiromasa, additional, Kosugi, Taichi, additional, Miyake, Takashi, additional, Ishibashi, Shoji, additional, Terakura, Kiyoyuki, additional, Medarde, Marisa, additional, Straessle, Thierry, additional, Pomjakushin, Vladimir, additional, Martínez-Lope, María Jesus, additional, Alonso, José Antonio, additional, Nowak, R., additional, Chrobak, D., additional, Gerberich, W. W., additional, Niihara, K., additional, Wyrobek, T., additional, Estradé, S., additional, Rebled, J. M., additional, Walls, M. G., additional, de la Peña, F., additional, Colliex, C., additional, Córdoba, R., additional, Infante, I. C., additional, Herranz, G., additional, Sánchez, F., additional, Fontcuberta, J., additional, Peiró, F., additional, Velessiotis, D., additional, Douvas, A. M., additional, Dimitrakis, P., additional, Argitis, P., additional, Glezos, N., additional, Chrobak, Dariusz, additional, Gerberich, William W., additional, Nowak, Roman, additional, Meyer, Carola, additional, Spudat, C., additional, Müller, M., additional, Houben, L., additional, Maultzsch, J., additional, Goss, K., additional, Thomsen, C., additional, Schneider, C. M., additional, Reza Golobostanfard, Mohammad, additional, Abdizadeh, Hossein, additional, Schmidt, Manuel J., additional, Engels, Stephan, additional, Epping, Alexander, additional, Trellenkamp, Stefan, additional, Wichmann, Uwe, additional, Stampfer, Christoph, additional, Rocha, Paulo R. F., additional, Chen, Qian, additional, Kiazadeh, Asal, additional, Gomes, Henrique L., additional, Meskers, Stefan, additional, de Leeuw, Dago, additional, Paßens, Michael, additional, Busiakiewicz, Adam, additional, Franz, Adam W., additional, Barkschat, Christa S., additional, Urselmann, Dominik, additional, Müller, Thomas J. J., additional, Soltow, A., additional, Karthäuser, S., additional, Waser, R., additional, Zeng, Fei, additional, Yang, Jing, additional, Wang, Zhishun, additional, Lin, Yisong, additional, Li, Sizhao, additional, Hirschfeld, Julian A., additional, and Lustfeld, Hans, additional

Published
2013
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