京都大学 / 新制・課程博士 / 博士(情報学) / 甲第25444号 / 情博第882号 / 新制||情||148(附属図書館) / 京都大学大学院情報学研究科通信情報システム専攻 / (主査)教授 佐藤 高史, 教授 橋本 昌宜, 教授 新津 葵一 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

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Ce projet vise à étudier, par une approche pluridisciplinaire, l’influence des la cristallisation des protéines membranaires (PM) en prenant pour protéine modèle le complexe photosynthétique RC-LH1-pufX de Rhodobacter blasticus. Des cristaux de ce complexe avaient été obtenus en présence de dodécyl-!-maltoside (DDM) et avaient diffractés à 8 Å de résolution. L’objectif final est de pouvoir améliorer, de façon rationnelle, la qualité des cristaux du complexe RC-LH1-pufX grâce à une meilleure compréhension des mécanismes mis en jeu. Dans un premier temps, trois tensioactifs dérivés du DDM ont été conçus et synthétisés. L’intérêt est d’augmenter la rigidité et le caractère lipophobe des parties hydrophobes des tensioactifs par rapport au DDM, pour les rendre moins déstabilisants envers la protéine: soit par l’incorporation d’un groupement bicyclohexyle (PCC-maltoside), soit par l’ajout d’un segment fluoré de longueur modulable (F4H5- et F2H9-maltoside). Nous avons inclus également le F8TAC, tensioactif fluoré utilisé depuis une vingtaine d’années pour le maintien en solution des PM, et les "tripodes", amphiphiles faciaux dont la géométrie particulière n’avaient jamais été testée. Nous avons ensuite réalisé la caractérisation physico-chimique, en solution, de ces tensioactifs et du DDM en terme de CMC (concentration micellaire critique), nombre d’agrégation, taille (par diffusion de la lumière dynamique, DLS), facteur de forme (par diffusion des rayons X aux petits angles, SAXS) et facteur de structure (par mesure du second coefficient du viriel, indicateur du potentiel des tensioactifs à initier la cristallisation)afin de déterminer les caractéristiques importantes au maintien en solution et à la cristallisation des PM. Le PCC-malt présentant le même comportement que le DDM,nous l’avons sélectionné pour réaliser une étude en présence de la protéine.Après avoir mis au point une méthode de dosage des tensioactifs par HPTLC (HighPerformance Thin Layer Chromatography) et identifier les lipides présents dans les de Rhodobacter blasticus, nous avons pu quantifier les quantités de lipides et de tensioactifs associés à la protéine en présence de DDM et de PCC-malt.Enfin, dans une dernière partie, nous avons réalisé des essais de cristallisation du complexe RC-LH1-pufX en présence des tensioactifs sélectionnés pour faire le lien entre les conditions de cristallisation et l’étude physico-chimique des micelles en solution. / Membrane proteins (MPs) are involved in the regulation of various fundamental cellular functions, such as cell recognition, receptor-mediated signal transduction and selective transportation of metabolites. However despite their huge importance, researches in MPs are relatively limited. For example MPs represent approximately 30% of the human proteome and less than 1% of current Protein Data Bank entries. Indeed, the presence of hydrophobic domains in MPs makes them not soluble in water. Therefore surfactants are used to extract MPs from their native environment and substitute for lipids around the transmembrane domain of the protein, forming water-soluble complexes. However MPs are often unstable in surfactant solution because of the intrusion of the alkyl chain of the surfactant into the transmembrane domain and/or the dissociation of stabilizing lipids, cofactors or subunits. Our project aims to study, through a multidisciplinary approach, the influence of surfactants for MP crystallization. Since dodecylmaltoside (DDM) is the most common gentle detergent used for MPs crystallization, we synthesized three new structurally DDM-derivative surfactants whose designs were expected to limit MPs inactivation. The objective was to increase the rigidity and the lipophobic behavior of the hydrophobic moiety by adding a bicyclohexyl group (PCC-maltoside) or using different lengths of fluorinated segments (F4H5- and F2H9-maltoside). Comparison of these surfactants with DDM occurs on:Physico-chemical properties: Surfactants are characterized by their CMC, molar mass (SEC-MALS, SAXS), hydrodynamic size (DLS), form factor (SAXS) and structure factor (A2, indicator of surfactant potential to lead to crystallization) in order to determine their best characteristics for MPs crystallization. Biochemical properties: We chose the RC-LH1-Puf X complex from Rhodobacter blasticus as model protein because of its biological interest. Besides this membrane protein has already been crystallized in DDM giving a low diffraction resolution (8Å). A better understanding of mechanisms involved in crystallization is a prerequisite for the development of rational approaches to increase crystals quality. Therefor protein complexes are characterized by quantifying lipids and surfactants bound to the transmembrane domain. Surfactant and lipid assays are performed by High Performance Thin Layer Chromatography (HPTLC). Crystallization trials: we show the link between crystallization and surfactants physico-chemical properties

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<p>The last few decades have witnessed unprecedented growth in multiple areas of electronics spanning low-power sensing, intelligent computing and high-speed wireless connectivity. In the foreseeable future, there would be hundreds of billions of computing devices, sensors, things and people, wherein the technology will become intertwined with our lives through continuous interaction and collaboration between humans and machines. Such human-centric ideas give rise to the concept of internet of bodies (IoB), which calls for novel and energy-efficient techniques for sensing, processing and secure communication for resource-constrained IoB nodes.As we have painfully learnt during the pandemic, point-of-care diagnostics along with continuous sensing and long-term connectivity has become one of the major requirements in the healthcare industry, further emphasizing the need for energy-efficiency and security in the resource-constrained devices around us.</p> <p>  </p> <p>  With this vision in mind, I’ll divide this dissertation into the following chapters. The first part (Chapter 2) will cover time-domain sensing techniques which allow inherent energy-resolution scalability, and will show the fundamental limits of achievable resolution. Implementations will include 1) a radiation sensing system for occupational dosimetry in healthcare and mining applications, which can achieve 12-18 bit resolution with 0.01-1 µJ energy dissipation, and 2) an ADC-less neural signal acquisition system with direct Analog to Time Conversion at 13pJ/Sample. The second part (Chapters 3 and 4) of this dissertation will involve the fundamentals of developing secure energy-efficient electro-quasistatic (EQS) communication techniques for IoB wearables as well as implants, and will demonstrate  2 examples: 1) Adiabatic Switching for breaking the αCV^2f limit of power consumption in capacitive voltage mode human-body communication (HBC), and 2) Bi-Phasic Quasistatic Brain Communication (BP-QBC) for fully wireless data transfer from a sub-6mm^3, 2 µW brain implant. A custom modulation scheme, along with adiabatic communication enables wireline-like energy efficiencies (<5pJ/b) in HBC-based wireless systems, while the BP-QBC node, being fully electrical in nature, demonstrates sub-50pJ/b efficiencies by eliminating DC power consumption, and by avoiding the transduction losses observed in competing technologies, involving optical, ultrasound and magneto-electric modalities. Next in Chapter 5, we will show an implementation of a reconfigurable system that would include 1) a human-body communication transceiver and 2) a traditional wireless (MedRadio) transceiver on the same integrated circuit (IC), and would demonstrate methods to switch between the two modes by detecting the placement of the transmitter and receiver devices (on-body/away from the body). Finally, in Chapter 6, we shall show a technique of augmenting security in resource-constrained devices through authentication using the Analog/RF properties of the transmitter, which are usually discarded as non-idealities in a digital transceiver chain. This method does not require any additional hardware in the transmitter, making it an extremely promising technique to augment security in highly resource-constrained scenarios. Such energy-efficient intelligent sensing and secure communication techniques, when combined with intelligent in-sensor-analytics at the resource-constrained nodes, can potentially pave the way for perpetual, and even batteryless systems for next-generation IoT, IoB and healthcare applications.</p>

<p dir="ltr">Unintentional electromagnetic emission (called emanation) from electronic devices and cables contains a significant correlation with the source signal and can be used to recover otherwise confidential data. In our work, EM emanation has been exploited to recover keystrokes from USB keyboards. Also, such emission has been utilized to form a covert channel for data exfiltration from air-gapped devices without being detected by IDS. To protect sensitive information, an automated emanation detection system has been proposed by developing two emanation detection algorithms (CNN-based and harmonic-based) through the characterization of emanation signals from a wide range of devices. Apart from emanation, data theft can happen due to the failure of access control methods. Traditional wireless devices are susceptible to various spoofing attacks as they only use digital signature-based authentication systems, ignoring the physical signatures completely. To circumvent that, RF-PUF was proposed to use device-specific signatures to be used for trust augmentation in traditional methods. By forming an extensive experimental dataset, we established RF-PUF as a strong PUF with a low-power overhead that outperformed the state-of-the-art methods and is robust against typical attacks. For real-time authentication, we proposed DIRAC, which forms dynamic device clusters and incrementally learns as more device data becomes available. Since our root of trust is in the physical signature of the ICs, they also need to be secured. However, counterfeited ICs may jeopardize that goal. We have proposed RF-PSF, which uses device-specific physical properties to authenticate its process technology which is a big part of the cloned IC detection.</p>