ED Mathématiques et Informatique
Study of quantum LDPC codes and their decoding
by Wouter ROZENDAAL (IMB - Institut de Mathématiques de Bordeaux)
The defense will take place at 14h30 - Salle 1 Institut de Mathématiques de Bordeaux Université de Bordeaux, Bâtiment A33 351, cours de la Libération F-33405 Talence, France
in front of the jury composed of
- Gilles ZéMOR - Professeur des universités - Université de Bordeaux - Directeur de these
- Valentin SAVIN - Directeur de recherche - CEA-Léti - Rapporteur
- Jean-Pierre TILLICH - Directeur de recherche - Inria de Paris - Rapporteur
- Benjamin AUDOUX - Professeur des universités - Aix-Marseille Université - Examinateur
- Elena BERARDINI - Chaire de professeur junior - Université de Bordeaux - Examinateur
- Cyril GAVOILLE - Professeur des universités - Université de Bordeaux - Examinateur
Quantum Low-Density Parity-Check (LDPC) codes provide a promising solution to protect quantum information from errors, and are therefore considered an important step in the realisation of a full-scale fault-tolerant quantum computer. In this thesis, we study quantum LDPC codes under three different approaches, providing insights in renormalisation decoding for Kitaev's toric code, establishing bounds on the minimum distance of geometrically-local codes, and constructing small instances of quantum Tanner codes. Kitaev's toric code is a prominent quantum LDPC code that is currently the most widely pursued for experimental implementation. We focus on the probabilistic renormalisation decoders introduced by Duclos-Cianci and Poulin, a family of decoders that exhibit one of the best trade-offs between accuracy and efficiency. We study how they handle adversarial errors by introducing a deterministic renormalisation decoder that does not use a priori probabilities of the error model. We find that this renormalisation decoder allows for fractal-like uncorrectable error patterns, and we obtain a lower bound on the weight of such errors. Due to physical constraints, a lot of attention has gone into quantum LDPC codes whose stabilisers act only on a limited number of nearby qubits. We extend the well known Bravyi-Terhal bound to quantum codes defined by local constraints on a lattice quotient, providing a crucial insight into the limitations of geometrically-local stabiliser codes. As an application, we provide upper bounds on the minimum distance of Abelian Two-Block Group Algebra codes, a family of quantum LDPC codes for which the minimum distance is currently unknown. In recent years, asymptotically good quantum LDPC codes were constructed, but provable results on their minimum distances only apply to impractically long codes. Following the effort in the design of near-term implementable codes, we construct short instances of quantum Tanner codes using square complexes obtained from lifted products of regular graphs. Several explicit instances of these codes exhibit minimum distances surpassing the square root of the code length.
ED Sciences de la Vie et de la Santé
PREFRONTAL NEURONAL POPULATIONS IN THREAT REPRESENTATIONS AND THE ORCHESTRATION OF DEFENSIVE BEHAVIORS
by Guillem LOPEZ-FERNANDEZ (Neurocentre Magendie)
The defense will take place at 14h30 - CARF/CGFB Building - Salle de Conférence 146 Rue Léo Saignat - CARF/CGFB - 33000 Bordeaux, France
in front of the jury composed of
- Cyril HERRY - Directeur de recherche - Université de Bordeaux - Directeur de these
- Jan GRüNDEMANN - Professor - Université de Bonn - Rapporteur
- Letzkus JOHANNES - Professor - Université de Fribourg - Rapporteur
- Daniela POPA - Directrice de recherche - Institut de Biologie de l'École normale supérieure (IBENS) - Examinateur
- Nikolas KARALIS - Chargé de recherche - Institut du Cerveau - Examinateur
- Lisa ROUX - Directrice de recherche - Université de Bordeaux - Examinateur
Behavior originates from the interaction between brain function, internal motivational demands, and environmental signals. Within this interplay, a crucial part of an animal's behavior is driven by the need to anticipate, detect and respond to environmental challenges such as danger. Responses to threat emerge from the organization of multiple interconnected brain regions into what is known as survival circuits of defense, among which the medial prefrontal cortex (mPFC) is a central regulator of defensive behavior. Most of the research on defensive systems over the last decades rely on classical conditioning paradigms, which, while providing immense insight into the neurobiology of aversive memories, are limited by their reductionist design. By studying a single threat and defensive response, these frameworks cannot model the complexity of behavior in more naturalistic settings, where organisms must dynamically evaluate multiple threats and integrate both aversive and rewarding signals to flexibly execute appropriate behaviors. Consequently, while the mPFC is known to integrate multimodal stimuli and exert precise control over complex behavior, its role in the flexible expression of context-appropriate coping strategies has been rarely addressed. Moreover, the literature has largely centered on the function of pyramidal neurons or mixed populations, whereas the less abundant yet functionally crucial GABAergic interneurons (INs) have received relatively little attention. To address these gaps, we used a recently introduced behavioral paradigm that exposes mice to distinct threats requiring specific defensive responses. By combining this task with electrophysiology, calcium imaging, optogenetic manipulations, and neuronal population and behavioral analyses, we examined the contribution of the dorsomedial PFC (dmPFC) and its distinct neuronal populations in the representation of threat-related information and the orchestration of defensive coping strategies. Our results demonstrate that the dmPFC encodes both general and specific representations of danger, and that its major inhibitory neuronal populations—namely somatostatin (SST) and parvalbumin (PV)-expressing interneurons—have different, yet complementary, roles in the representation of threatening and non-threatening conditions and the execution of defensive behaviors. While SST-INs contribute to the refinement of threat discrimination and to resolving stimulus uncertainty, PV-INs convey the general detection of emotionally-salient stimuli to mediate transitions from basal to aversive states. In addition, by using behavioral segmentation onto defensive responses, we show that distinct defensive strategies arise from sequences of discrete behavioral motifs that are distinctly and dynamically encoded in the dmPFC. Our findings elucidate that appropriate coping strategies depend on specific, non-stationary dmPFC activity patterns that promote the flexible arrangement of these motifs into context-adapted behavioral sequences, whereas stationary activity patterns are associated with rigid behavioral patterns and inappropriate coping strategies. This underscores a key computational process by which altered dmPFC activity may underlie core features of cognitive and behavioral inflexibility observed across multiple fear- and anxiety-related disorders.
ED Sciences Physiques et de l'Ingénieur
Development of Organic Electrochemical Transistors (OECTs) for Biological Applications
by Reem EL ATTAR (Laboratoire de l'Intégration du Matériau au Système)
The defense will take place at 9h30 - Amphithéâtre Jean Paul DOM A0.85 351 Cours de la Libération, Bâtiment A31 (IMS) 33405 Talence Cedex, France
in front of the jury composed of
- Mamatimin ABBAS - Chargé de recherche - Université de Bordeaux - Directeur de these
- Damien THUAU - Maître de conférences - Bordeaux INP - CoDirecteur de these
- Fabio BISCARINI - Professeur - Università degli Studi di Modena e Reggio Emilia - Rapporteur
- Sylvie RENAUD - Professeure - IMS laboratory - Examinateur
- Esma ISMAILOVA - Maîtresse de conférences - Ecole Nationale Supérieure des Mines de Saint Etienne - Rapporteur
- Vincent NOEL - Professeur des universités - Université Paris cité - Examinateur
The evolution of bioelectronic devices based on organic materials is bridging the gap between organic semiconductor-based electronics and the ionic nature of biological systems. Among these devices, Organic Electrochemical Transistors (OECTs) have emerged as particularly promising due to their high transconductance and excellent signal-to-noise ratio, making them suitable for detecting weak biological signals. This PhD thesis focuses on the fabrication and characterization of OECTs for biological applications. Devices were microfabricated in the cleanroom by photolithography process, and the conducting polymer channel was deposited using electropolymerization, a technique chosen for its advantages in localized deposition, dopant incorporation, and tunability of film properties. Several functional monomers were electropolymerized and their performance as organic mixed ionic electronic conductor in OECT were investigated: After an initial effort of establishing electro-polymerization setup, EDOT (3,4-ethylenedioxythiophene) was electropolymerized. The resulting PEDOT-based OECTs exhibited high transconductance (gm max ~ 12 mS), and remained stable in biological medium over several days. Cardiomyocyte-like (HL-1) cells were grown on the OECT channel to validate the performance of the OECTs and the experimental setup for monitoring cellular electrical activity. In parallel, a zinc-selective thiophene based trimer with a Dipicolylamine (Tri-DPA), was used to fabricate Zn²⁺-specific sensors, for the detection of zinc ion flux during insulin secretion from pancreatic β-cells in pancreatic islets. OECTs specific to Zinc ion were obtained, with a limit of detection (LoD) of about 1.5 µM, showing promising results for extracellular electrical activity recording of β-cells. Moreover, electropolymerization of an n-type monomer was performed, with the aim of fabricating and characterizing n-type OECTs, eventually to integrate these n-type devices with p-type OECTs to create complementary circuits, which are promising for biological applications. This monomer bares a naphthalene diimide core with thiophene functional group, destined to do anodic electropolymerization to facilitate the deposition process. Despite the challenges usually associated with n-type polymers, successful electropolymerization in OECT channels was achieved. Experiments were conducted to enhance the properties of the polymer film by studying the effect of the solvents, the monomer concentration, and the size of working electrode. Although no gate modulation has been observed, extensive insights have been gained to guide the future development of n-type electropolymerized OECTs. This thesis work aimed to advance the development of functional OECT-based sensors for applications in both electrophysiological recording and ion detection, while also laying the groundwork for the integration of complementary circuits in future bioelectronic systems.