Nonequilibrium Properties of Strongly Correlated One-dimensional Quantum Gases

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyUnderstanding and controlling nonequilibrium quantum systems offers promising routes to applications unattainable in equilibrium systems. While equilibrium physics benefits from well-established approaches, such as minimizing free energy and obtaining various thermodynamic quantities, nonequilibrium systems possess less general guiding principles and approaches. Furthermore, strong correlations plays a crucial role in various quantum phenomena, such as high-temperature superconductors or superfluid helium, yet analyzing strongly correlated quantum systems remains exceedingly challenging. This is because these systems often require rigorous analysis beyond the standard perturbation theory, leading to the necessity of dealing with the large Hilbert space dimensions, which makes theoretical analysis difficult. However, in the case of a one-dimensional strongly interacting Bose gas called Tonks–Girardeau (TG) gas, an exact mapping to a noninteracting fermions is possible, providing a unique platform to study a strongly correlated many-body systems. This thesis aims to advance the theoretical understanding of nonequilibrium strongly correlated quantum systems from two distinct perspectives: integrability and Floquet physics. First, I investigate the nonequilibrium dynamics of strongly correlated TG bosons immersed in a weakly correlated Bose–Einstein condensate. I show that the TG bosons form an integrable soliton-train supported by the condensate. Moreover, since a gas of the noninteracting fermions follows the same governing equations, the quantum statistical nature of the soliton-train can be addressed, leading to the notion of a quantum soliton-trains. Next, I study the TG gas under a strong external time-periodic drive. By computing the nonequilibrium Green’s function exactly, I reveal the excitation spectrum of this Floquet-engineered material. Employing Floquet spectral function theory and the Bose–Fermi mapping theorem, I uncover the existence of nonequilibrium Lieb excitations when the underlying mapped fermions form a Floquet–Fermi sea.doctoral thesi

Biologically Plausible Synaptic Plasticity Model for Rapid Neuronal Tuning

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyIn the intricate workings of the brain, neurons play a fundamental role in detecting meaningful patterns amidst a constant stream of information. However, the rapidity with which neurons accomplish this task often goes unnoticed in computational models, leading to a gap in understanding crucial mechanistic features observed in biological neurons. To bridge this gap, I introduce a class of neural models equipped with a biologically-inspired synaptic plasticity rule. The aim of this thesis research is to shed light on the brain’s ability to rapidly learn and discern statistically salient patterns. My approach leverages the dynamic interplay between neural activity and synaptic plasticity, where somatic spikes propagate back to dendrites, facilitating self-supervised detection and learning of presynaptic neuron communities impinging on dendrites. I showcase the efficacy of these models in various tasks, including pattern recognition and spatial navigation, where they establish swift associations between behavior and environmental cues. Moreover, in exploring multi-compartmental neural architectures, I extend the synaptic plasticity rule to elucidate the initiation and development of local dendritic spikes, offering insights into neural processing mechanisms. My modeling work underscores the importance of pre-existing neural assemblies in robust pattern learning within recurrent networks. By illuminating the self-supervision function of backpropagating action potentials and the role of pre-existing neural assemblies, my findings contribute to a deeper comprehension of brain cognitive function and its implications for artificial intelligence and neuroscience.doctoral thesi

Identification of Functional miRNAs Regulating Plasma Membrane Damage-dependent Senescence in Human Fibroblasts

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyDamage to the plasma membrane is common in nature, caused by a variety of triggers ranging from physical damage to cell-autonomous activities. Our previous study has revealed that cellular senescence, a state of irreversible cell cycle arrest that contributes to organismal aging, is one of the cellular outcomes that can be triggered by plasma membrane damage. Upon the induction of plasma membrane damage-dependent senescence (PMD-Sen), human diploid fibroblasts exhibit senescence features, including increased β-galactosidase activity, the manifestation of senescence-associated secretory phenotypes, and the upregulation of senescence marker proteins, including p53, p21, and p16. However, the molecular mechanisms underlying PMD-Sen remain unclear. Given that substantial alterations in gene expression are associated with the onset of senescence, it is essential to investigate the regulatory mechanisms responsible for gene expression changes during cellular senescence. MicroRNAs (miRNAs), a large class of small noncoding RNAs, have been identified as critical regulators of gene expression by targeting messenger RNAs (mRNAs). When miRNAs bind to the 3’ untranslated region (3’UTR) of target mRNAs, they primarily inhibit translation or promote degradation of the target mRNAs. In this study, to identify regulatory miRNA-mRNA pairs in PMD-Sen cells, I performed an integrated analysis of miRNA and mRNA expression profiles in a time-resolved manner. My analysis suggests that a total of 2495 miRNA-mRNA pairs, comprising 65 miRNAs, are involved in the process of PMD-Sen. The results support the hypothesis that miRNAs regulate senescence induction by post-transcriptionally regulating their target mRNAs. Furthermore, an overlap was identified between the set of miRNA-mRNA pairs implicated in PMD-Sen and DNA damage-induced senescence (DDR-Sen), leading to the identification of 41 shared miRNAs in the pairs. This suggests common regulatory miRNA-mRNA pairs across different senescent cell subtypes. Notably, miR-155-5p emerged as the miRNA with the largest number of shared miRNA-mRNA pairs that exhibit a highly negative correlation. These findings imply that miR-155-5p may have a role in PMD-Sen and DDR-Sen.doctoral thesi

Comprehensive Identification of Plasma Membrane Repair Proteins Uncovered the Clathrin-mediated Endocytosis-dependent Repair Protein Delivery Mechanisms

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyDamage to the plasma membrane (PM) is common in living cells. Virtually all cells have mechanisms to repair the damaged PM. One of the evolutionarily conserved PM repair processes is targeting proteins, defined as PM repair proteins, to the damage site. PM repair proteins play critical roles in the PM repair processes. However, the mechanisms underlying the repair protein delivery to the damage site are largely unexplored. Moreover, identifying new repair proteins remains challenging in this field. In this thesis, I addressed these issues using budding yeast Saccharomyces cerevisiae as a model. In the first project, I revealed that clathrin-mediated trafficking of phospholipid flippases is required for PM/cell wall repair in budding yeast. In addition, the deletion of phospholipid flippases impaired the accumulation of exocyst, which functions to dock exocytic vesicles with the PM at the damage site. I propose the model that phospholipid flippases remodel the lipid composition at the damage site, thereby facilitating the binding of exocyst to the PM. In the second project, I performed a high-throughput visual screening using yeast GFP collections, which cover ~90 % (5,718 ORFs) of yeast ORFs to comprehensively identify the repair proteins. I identified 564 proteins whose localization changed in response to the PM-damaging chemical SDS. The laser damage assay identified 80 proteins accumulated at the damage site, including 72 previously unidentified repair protein candidates. By quantifying the fluorescence intensity at the damage site over time, I revealed the functional order of repair proteins. Among the identified repair proteins, those involved in clathrin-mediated endocytosis (CME) were required for yeast growth in conditions that induce PM/cell wall damage. I found that CME proteins are required for polarized exocytosis at the damage site and for the transportation of PM proteins from the growing bud site to the damage site. In addition, one of the CME cargoes, Snc1, was recovered from the damage site to the growing bud site, presumably via CME. Given that these processes occur from 2min after the damage, CME may restructure the damaged PM after resealing. I propose the model that CME restructures the damaged PM by regulating the amount of PM proteins at the damage site.doctoral thesi

On the Analysis of Collective Dynamics in Social Groups with Bees and Football Players as Case Studies

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe main focus of this thesis is investigating the emergent effects observed in the collective dynamics of the honeybee hive. We use a previously acquired dataset of time-resolved trajectories of hundreds of bees inside the hive, recorded for multiple days and nights. In a series of papers, we study the temporal and spatial dynamics of the bee hive, uncovering scale-free correlations of occupancy fluctuations in both temporal and spatial domains. These observations indicate the proximity of the system to the second-order phase transition. Furthermore, we observe a non-trivial relationship between throughput and density, implying that the beehive undergoes a jamming transition. This finding is explored further by constructing a model of jamming in 2D using stochastic cellular automata and exploring how correlation length is dependent on the density. Additional insights are obtained by studying the properties of the functional network computed using correlations between the timeseries of individual bees. The supplementary project is centered on the study of the trajectories of professional football players from the Japanese football league. It has been found that statistical properties of trajectories of individual players’ are best described by the Lévy walk dynamics. Furthermore, we have found that these dynamics are preserved when centers of mass trajectories for each team are considered. However, the power-law distribution of step sizes which is indicative of the Lévy walk is reduced to the exponential when only the periods when players are in possession of the ball are considered. Based on these findings we hypothesize that players’ behavior is reminiscent of that of the foraging animals which resort to Lévy walk when resource distribution is sparse.doctoral thesi

Anatomical and Functional Study of the Superior Colliculus Pathway to the Inferior Olive in Mice

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe Inferior olive is an important region for motor learning and movement coordination. Its climbing fiber projections to Purkinje neurons drive complex spike activity, a central element in cerebellar function theories. Although the function of the inferior olive has been investigated by the occurrence of complex spikes during motor learning, it remains unclear how its intrinsic properties and activity shape the generation of complex spikes upon receiving sensory stimulation. To investigate how signals from a pre-olivary structure with a well-defined behavioral role affect IO spiking, I focused on an afferent from the midbrain superior colliculus. The superior colliculus is an evolutionarily conserved midbrain region known for its role in mediating orienting-related movements. The SC-IO pathway serves as an excellent model for studying how inferior olive neurons (IO) respond to their inputs. Additionally, this pathway raises the exciting possibility for orienting-related behaviors modulated by learning through the olivo-cerebellar system. In this study, we explore SC projections to the IO using viral tracers, calcium imaging, and optogenetic stimulation. In addition to the established projections to the medial accessory olive (MAO), we uncover SC axonal projections to the ventral principal olive (PO). Our findings reveal that SC axons terminate on both dendritic shafts and spines of IO neurons, potentially influencing the probability of spike and the network synchronization mediated by gap junctions on dendritic spines. To demonstrate the ability of SC axons to drive IO spiking, we performed in vivo calcium imaging and showed that optogenetic activation of SC inputs not only induces spiking, but also modulates the overall synchronization of the IO. This study lays a foundational framework for exploring the behavioral relevance of the SC-IO pathway in mice.doctoral thesi

Characterizing the sense of agency in human–robot interaction based on the free energy principle

Social interaction takes various forms, ranging from cooperation to conflict. The current study focused on competition between top-down and bottom-up information processes in perception and action generation in social interaction, based on the free energy principle. In particular, it attempted to account for the sense of agency. We built a computational model for multimodal social interaction with a variational Bayes recurrent neural network, based on the free energy principle, and we evaluated the model in imitative interaction between a human and a robot. Our findings demonstrate that when prioritization of the top-down process is enhanced, the robot behaves egocentrically, leading the human more and manifesting a stronger sense of agency. Conversely, when this prioritization is reduced, the robot tends to modify its intention so that it aligns with that of its human counterpart, suggesting a weaker sense of agency. We also proposed a computational model for a multifactorial account of the sense of agency and examined the correspondence between the experimental results and the model. The study reveals the underlying mechanism of social interaction dynamics and the resultant sense of agency by conducting a rigorous analysis of the neural internal representation, as well as the behaviors of the human and the robot.journal articl

Predicting Future Ant Invasions and Assessing Community Dynamics After Establishment

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyAs humans have spread and increasingly dominated the planet, other species have also been introduced to places beyond their natural dispersal capacity. Some of these species have become costly invasives causing severe damage in human lives and producing negative impacts on the environment and native biodiversity. Invasive ants are among the most damaging invasive species, with hundreds of species known to be spreading around the world. In this dissertation I study pre-establishment risks and post-establishment long term effects from a community perspective using the whole ant family (Hymenoptera: Formicidae). In the first chapter, I include relevant background information to the topic and study systems. In the second chapter, I forecast the risk of establishment for Japan from the global pool of alien ants. I derive potential source hotspots from around the globe using a new workflow built around species distribution modeling. These predictions are intended to help policy-makers implement better preventive programs for cargo coming from different regions of the world. I show that there is a latitudinal effect on the invasion risk and that the remote islands of Japan are at highest risk. The species identified as threats are most numerous in temperate European areas and the subtropical American continent, which could become the main sources of new invasive species to different regions of Japan. In the third chapter, I investigate how seasonality and land cover differences shape the spatial and temporal activity density of ant communities of different historical presence (native vs. alien) to the island of Okinawa in Japan using a hierarchical joint species distribution modeling approach. I demonstrate that, even long after the first introduction, alien ants have a distinct usage of the environment than native ants. Native species' activity is mainly driven by high temperatures with a strong phenological effect which results in high activity during spring and summer. Meanwhile alien species' activity have more types of responses to temperature and humidity, with most of them active at the colder and less humid seasons. Species are also spatially structured by land cover, as expected from invasion ecology, native species are most active in forested areas while alien species dominate urban environments, and both guilds are similarly active in open areas like agricultural land. In the fourth chapter, I include how these studies may be followed, general conclusions and highlight the need for extra preventive measures as the number of potential new invaders is higher than current invaders and past invasions show that alien species are able to exploit niches that native ants cannot, and include potential avenues to continue these research studies.doctoral thesi

The Evolution of Ant Mandibles & Advancing Comparative Morphology in 3D

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe diversity of life manifests in the countless forms of organisms, which are a key to understanding natural selection, the interface between genomes and the environment, and functional traits. Ants evolved a broad trophic spectrum and perform vastly different behaviors, universally exhibit a social lifestyle, their range of body plans is highly disparate, and they dominate terrestrial ecosystems. However, despite success in diversification and abundance, we lack an understanding of the factors that promote their morphological diversification or the functional constraints and tradeoffs that incur in ant evolution. In this thesis, I focus on a broad comparative study on the mandibles as the primary tools that ants use in social, environmental, and dietary interactions. I further developed workflows for phenotyping anatomy and spearheaded an initiative, which lays out how to obtain much more standardized 3D anatomical data suitable for automated methods than previously possible. In summary, chapter one of the thesis mainly addresses the solidification of automated muscle analysis based on CT-data. Central to chapter two is Antscan, a pilot project for creating digital libraries of 3D invertebrate anatomy based on high-throughput synchrotron µCT. Based on segmented data for over 600 individual ants, in chapter three, I found that the triangular ant mandible is a ground plan, which ants have mostly retained and remained conservative with. However, convergently evolved shapes driven by functional demands advantageous in predation and division of labor account for overall high morphological diversity. In this thesis, I unraveled contrasts among dimensions of diversity and enabled further research into 3D insect morphology by providing data directly and documenting how to obtain and analyze it and I hope that this work will make a useful contribution to biodiversity science.doctoral thesi

Cholinergic Interneurons of the Dorsomedial Striatum Mediate Winner-Loser Effects on Social Hierarchy Dynamics in Male Mice

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe overall aim of the research reported in this thesis is to investigate the phenomena and putative mechanisms of flexibility in the social hierarchy of male mice (C57BL7/J and heterozygous ChAT-cre mice). A social hierarchy is an organization of individuals by rank that occurs in social animals. Establishing a new social hierarchy involves flexible behavior in deciding, when competing with other animals, whether to be a winner or loser, responding to the experience of winning or losing, and subsequent stabilization of rank. The neural circuits underlying such flexible behavior have yet to be fully understood. Previous research indicates that cholinergic interneurons in the dorsomedial striatum play a role in various forms of behavioral flexibility. I hypothesize that similar mechanisms may be involved in social hierarchy dynamics. To investigate the effects of the experience of winning and losing on the social hierarchy, I used the dominance tube test to measure ranking within group housed mice, before and after between-cage competitions using the same test. I found that the experience of winning or losing against mice from different cages not only contributes to new social hierarchies among the competitors, but also causally influences the subsequent social hierarchy among their cage mates in the home cage – supporting the hypothesis of winner-loser effects on later social ranking. To test the hypothesis that cholinergic interneurons contribute to social hierarchy dynamics, I made a selective lesion of cholinergic interneurons in the dorsomedial striatum. The lesion did not prevent social hierarchy formation among pairs of similarly ranked individuals from different cages. However, it reduced the loser effect of external competition on the subsequent home-cage rankings in dominant mice. These findings support the concept of winner-loser effects on subsequent competition, and which suggest that cholinergic interneurons in dorsomedial striatum increase the flexibility of social hierarchy dynamics.doctoral thesi