京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第21550号 / 理博第4457号 / 新制||理||1640(附属図書館) / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)准教授 戸塚 圭介, 教授 川上 則雄, 教授 前野 悦輝 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

Reliable signal transmission among cells is important for long-range coordination. While higher organisms have designated structures for signal transmission, such as axons, it remains unclear how simpler communities of cells are organized to relay signals. Furthermore, many biological systems exhibit spatial heterogeneity, which can interrupt signal propagation. In this thesis, we investigate this problem by modeling the spatial organization and dynamics of electrochemical signaling, and we compare our results to experiments from our collaborators on Bacillus subtilis bacterial biofilms. The experiments show that only a fraction of cells participates in signal propagation and that these cells are spatially clustered with a size distribution that follows a power-law decay. These observations suggest that the fraction of participating cells is just at the tipping point between a disconnected and a fully connected conduit for signal transmission. We utilize percolation theory and a minimal FitzHugh-Nagumo-type excitable dynamics model to test this hypothesis, and genetically modified biofilms with altered structure and dynamics to validate our modeling. Our results suggest that the biofilm is organized near the critical percolation point in order to negotiate the benefit and cost of long-range signal transmission. Then, more detailed experiments show that the participation probability is correlated from cell to cell and varies in space. We use these observations to develop an enhanced percolation model, and show using simulations and a renormalization argument that the main conclusions are unaffected by these features. Finally, we use our dynamic model to investigate the effects of heterogeneity beyond the radial wave regime and into the spiral wave regime. We find that spatial correlations in the heterogeneity promote or suppress spiraling depending on the parameters, a surprising feature that we explain by demonstrating that these spirals form by distinct mechanisms. We characterize the dependence of the spiral period on the heterogeneity using techniques from percolation theory. Taken together, our results reveal that the spatial structure of cell-to-cell heterogeneity can have important consequences for signal propagation in cellular communities.<br>

abstract: Longitudinal studies contain correlated data due to the repeated measurements on the same subject. The changing values of the time-dependent covariates and their association with the outcomes presents another source of correlation. Most methods used to analyze longitudinal data average the effects of time-dependent covariates on outcomes over time and provide a single regression coefficient per time-dependent covariate. This denies researchers the opportunity to follow the changing impact of time-dependent covariates on the outcomes. This dissertation addresses such issue through the use of partitioned regression coefficients in three different papers. In the first paper, an alternative approach to the partitioned Generalized Method of Moments logistic regression model for longitudinal binary outcomes is presented. This method relies on Bayes estimators and is utilized when the partitioned Generalized Method of Moments model provides numerically unstable estimates of the regression coefficients. It is used to model obesity status in the Add Health study and cognitive impairment diagnosis in the National Alzheimer’s Coordination Center database. The second paper develops a model that allows the joint modeling of two or more binary outcomes that provide an overall measure of a subject’s trait over time. The simultaneous modelling of all outcomes provides a complete picture of the overall measure of interest. This approach accounts for the correlation among and between the outcomes across time and the changing effects of time-dependent covariates on the outcomes. The model is used to analyze four outcomes measuring overall the quality of life in the Chinese Longitudinal Healthy Longevity Study. The third paper presents an approach that allows for estimation of cross-sectional and lagged effects of the covariates on the outcome as well as the feedback of the response on future covariates. This is done in two-parts, in part-1, the effects of time-dependent covariates on the outcomes are estimated, then, in part-2, the outcome influences on future values of the covariates are measured. These model parameters are obtained through a Generalized Method of Moments procedure that uses valid moment conditions between the outcome and the covariates. Child morbidity in the Philippines and obesity status in the Add Health data are analyzed. / Dissertation/Thesis / Doctoral Dissertation Statistics 2020

In this work, optical pump – near-infrared probe and near-infrared pump – mid-infrared probe spectroscopy are used for the investigation of pressure-induced insulator-to-metal transitions in transition metal oxide compounds. The materials under study are α-Fe₂O₃, also known as hematite, and VO₂. Both materials undergo pressure-induced metallization. However, the physical mechanisms of this phase transition are very different for these systems and have not been fully understood up to now. Using ultrafast pump-probe spectroscopy we obtain an insight into the evolution of the band structure and electron dynamics across the insulator-to-metal transition. In the case of VO₂, our near-infrared pump – mid-infrared probe experiments reveal a non-vanishing pumping threshold for photo-induced metallization even at our highest pressures around 20 GPa. This demonstrates the existence of localized charge carriers and the corresponding persistence of a band gap. Besides the threshold behaviour for photo-induced metallization, the carrier relaxation time scale, and the linear reflectivity and transmissivity have been studied under pressure increase. An anomaly in the threshold behaviour as well as the linear reflectivity and transmissivity at a critical pressure around 7 GPa indicates band gap filling under pressure. This is further supported by results obtained under decompression, where the changes of the linear reflectivity turned out to be almost fully reversible. The observations on VO₂ are highly reproducible and can be explained in terms of a pressure-induced bandwidth-driven insulator-to-metal transition. Fe₂O₃ has been studied via optical pump – near-infrared probe spectroscopy up to pressures of 60 GPa. In the pressure range up to 40 GPa, the changes of the response can be explained by photo-induced absorption and bleaching. The pressure dependent study of the relaxation dynamics allows to identify cooling of the electron system as origin of the picosecond relaxation process. A sharp anomaly found in the response of Fe₂O₃ at 40 GPa indicates a strong rearrangement of the electronic band structure which could be explained by an insulator-to-metal phase transition induced by pumping. The successful demonstration of pump-probe experiments in diamond anvil cells using pulses from optical to mid-infrared wavelengths and reaching pressures of several tens of GPa is a good basis for further experimental high-pressure studies. Our results obtained on VO₂ and Fe₂O₃ can serve as a benchmark for the development of advanced material models. / In der vorliegenden Arbeit wird der druckinduzierte Isolator–Metall-Phasenübergang in den Übergangsmetalloxiden α-Fe₂O₃ (Hämatit) und VO₂ mittels ultraschneller Anrege-Abfrage-Spektroskopie (engl. pump-probe spectroscopy) untersucht. Hämatit wird dazu im sichtbaren Spektralbereich angeregt und im nahen Infrarot (NIR) abgefragt, bei VO₂ wurde zur Anregung NIR und zur Abfrage mittleres Infrarot (MIR) verwendet. Beide Materialien werden bei hinreichend hohem Druck metallisch, wobei die jeweils dem Isolator–Metall-Phasenübergang zugrundeliegenden Mechanismen verschieden und noch nicht vollständig verstanden sind. Dies motiviert den Einsatz von ultraschneller Anrege-Abfrage-Spektroskopie, die einen Einblick in die Änderung der Bandstruktur und der Ladungsträgerdynamik während des Isolator–Metall-Übergangs gewährt. Beim Überschreiten eines Schwellenwertes der Anregung wird VO₂ photoinduziert metallisch. In unseren NIR-MIR Anrege-Abfrage-Experimenten zeigt sich, dass der Schwellenwert auch bei den höchsten Drücken dieser Messreihe (ca. 20 GPa) nicht verschwindet. Dies weist auf die Existenz lokalisierter Ladungsträger hin und damit verbunden auf das Fortbestehen der Bandlücke. Neben dem Schwellenwert für photoinduzierte Metallisierung wurden auch die Druckabhängigkeiten der Relaxationsdynamik der Ladungsträger sowie des linearen Reflexions- und Transmissionsvermögens untersucht. Eine Anomalie im druckabhängigen Verlauf des Anrege Schwellenwertes sowie des linearen Reflexions- und Transmissionsvermögens bei einem kritischen Druck von ca. 7 GPa deutet darauf hin, dass durch das Anlegen von Druck Zustände innerhalb der Bandlücke induziert werden. Diese Interpretation wird auch durch während der Dekompression gewonnene Messdaten unterstützt. Die druckinduzierte Änderung des linearen Reflexionsvermögens erwies sich als nahezu vollständig reversibel. Unsere Beobachtungen an VO₂ sind reproduzierbar und lassen sich als druckinduzierter, Bandbreiten-getriebener Isolator–Metall-Übergang nachvollziehen. Fe₂O₃ wurde mittels Anrege-Abfrage-Spektroskopie bei Drücken bis zu 60 GPa untersucht. Änderungen im Druckbereich bis 40 GPa können als Wechselspiel eines photo-induzierten Absorptionsbandes und der photoinduzierten Unterdrückung eines anderen Absorptionskanals erklärt werden. Die druckabhängige Untersuchung der Relaxationsdynamik ermöglicht es, der Relaxation auf der Zeitskala weniger Pikosekunden Kühlungsdynamik als Ursache zuzuordnen. Eine scharfe Anomalie im qualitativen Verlauf des Anrege-Abfrage-Signals von Fe₂O₃ bei einem Druck von 40 GPa weist auf deutliche Änderungen in der elektronischen Bandstruktur hin, welche als Signatur eines photoinduzierten Isolator–Metall Phasenübergangs interpretiert werden können. Die erfolgreiche Demonstration von Anrege-Abfrage-Experimenten in Diamantstempeldruckzellen mit Laserimpulsen vom sichtbaren Spektralbereich bis hin zum mittleren Infrarot und bei Drücken von 20 GPa bis zu 60 GPa liefert die solide Basis für weitergehende Hochdruck-Experimente. Die an VO₂ und Fe₂O₃ erzielten Ergebnisse sind eine gute Grundlage für die Weiterentwicklung der theoretischen Beschreibung solcher Materialsysteme.

Fluid antenna systems (FAS) are an emerging technology that promises a signif icant diversity gain even in the smallest spaces. Motivated by the groundbreaking potentials of liquid antennas, researchers in the wireless communication community are investigating a novel antenna system where a single antenna can freely switch positions along a small linear space to pick the strongest received signal. However, the FAS positions do not necessarily follow the ever-existing rule separating them by at least half the radiation wavelength. Previous work in the literature param eterized the channels of the FAS ports simply enough to provide a single-integral expression of the probability of outage and various insights on the achievable perfor mance. Nevertheless, this channel model may not accurately capture the correlation between the ports, given by Jake’s model. This work builds on the state-of-the-art and accurately approximates the FAS channel while maintaining analytical tractabil ity. The approximation is performed in two stages. The first stage approximation considerably reduces the number of multi-fold integrals in the probability of outage expression, while the second stage approximation provides a single integral represen tation of the FAS probability of outage. Further, the performance of such innovative technology is investigated under a less-idealized correlation model. Numerical results validate our approximations of the FAS channel model and demonstrate a limited performance gain under realistic assumptions. Further, our work opens the door for future research to investigate scenarios in which the FAS provides a performance gain compared to the current multiple antennas solutions.

High resolution transient/3D imaging technology is of high interest in both scientific research and commercial application. Nowadays, all of the transient imaging methods suffer from low resolution or time consuming mechanical scanning. We proposed a new method based on TCSPC and Compressive Sensing to achieve a high resolution transient imaging with a several seconds capturing process. Picosecond laser sends a serious of equal interval pulse while synchronized SPAD camera's detecting gate window has a precise phase delay at each cycle. After capturing enough points, we are able to make up a whole signal. By inserting a DMD device into the system, we are able to modulate all the frames of data using binary random patterns to reconstruct a super resolution transient/3D image later. Because the low fill factor of SPAD sensor will make a compressive sensing scenario ill-conditioned, We designed and fabricated a diffractive microlens array. We proposed a new CS reconstruction algorithm which is able to denoise at the same time for the measurements suffering from Poisson noise. Instead of a single SPAD senor, we chose a SPAD array because it can drastically reduce the requirement for the number of measurements and its reconstruction time. Further more, it not easy to reconstruct a high resolution image with only one single sensor while for an array, it just needs to reconstruct small patches and a few measurements. In this thesis, we evaluated the reconstruction methods using both clean measurements and the version corrupted by Poisson noise. The results show how the integration over the layers influence the image quality and our algorithm works well while the measurements suffer from non-trival Poisson noise. It's a breakthrough in the areas of both transient imaging and compressive sensing.

This paper reports a study of the inheritance and of the correlated inheritance in certain observed and measured plant characters in a cross between a hybrid from Dicklow x sevier, (F22) and a pure line from Dicklow, (D#3), one of the original parents of F 22.

RSS-based localization is a promising solution for estimating the position of a non-collaborative emitter using a network of collaborative sensors. This paper examines RSS-based localization and differential RSS (DRSS) localization in the presence of correlated shadowing with no knowledge of the emitter's reference power.  A new non-linear least squares (NLS) DRSS location estimator that uses correlated shadowing information to improve performance is introduced. The existing maximum likelihood (ML) estimator and Cram\' er Rao lower bound (CRLB) for RSS-based localization given do not account for correlated shadowing. This paper presents a new ML estimator and CRLB for RSS-based localization that account for spatially correlated shadowing and imperfect knowledge of the emitter's reference power. The performance of the ML estimator is compared to the CRLB under different simulation conditions. The ML estimator is shown to be biased when the number of sensors is small or the shadowing variance is large. The effects of correlated shadowing on an RSS-based location estimator are thoroughly examined. It is proven that an increase in correlated shadowing will improve the accuracy of an RSS-based location estimator. It is also demonstrated that the ideal sensor geometry which minimizes the average error becomes more compact as correlation is increased. A geometric dilution of precision (GDOP) formulation is derived that provides a metric for the effect of the position of the sensors and emitter on the location estimator performance. A measurement campaign is conducted that characterizes the path loss at 3.4 GHz. The measurements are compared to the log-distance model. The errors between the model and the measurements, which should theoretically be Gaussian, have a Kurtosis value of 1.31. The errors were determined to be spatially correlated with an average correlation coefficient of 0.5 at a distance of 160 meters. The performance of the location estimators in simulation is compared to the performance using measurements from the measurement campaign. The performance is very similar, with the largest difference between the simulated and actual results in the ML estimator. In both cases, the new NLS DRSS estimator outperformed the other estimators and achieved the CRLB. / Master of Science

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第21548号 / 理博第4455号 / 新制||理||1640(附属図書館) / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 川上 則雄, 教授 田中 耕一郎, 教授 前野 悦輝 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18062号 / 理博第3940号 / 新制||理||1568(附属図書館) / 30920 / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 川上 則雄, 教授 石田 憲二, 准教授 藤本 聡 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM