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Bifractal nature of chromosome contact maps
Get PDFModern biological techniques such as Hi-C permit one to measure probabilities that different chromosomal regions are close in space. These probabilities can be visualized as matrices called contact maps. In this paper, we introduce a multifractal analysis of chromosomal contact maps. Our analysis reveals that Hi-C maps are bifractal, i.e., complex geometrical objects characterized by two distinct fractal dimensions. To rationalize this observation, we introduce a model that describes chromosomes as a hierarchical set of nested domains and we solve it exactly. The predicted multifractal spectrum is in excellent quantitative agreement with experimental data. Moreover, we show that our theory yields a more robust estimation of the scaling exponent of the contact probability than existing methods. By applying this method to experimental data, we detect subtle conformational changes among chromosomes during differentiation of human stem cells.journal articl
Control and measurement of non-classical properties of cold atomic and optical systems
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyI present the work done during my PhD in the field of quantum gases, metrology, and thermodynamics, which aims at revealing and controlling non-classical correlations and features in various systems. First, I have studied two strongly interacting bosons with synthetic spin-orbit coupling. In this work, I have described the ground state beyond the mean-field regime and explored the existence of non-classical correlations. In a second project, I have investigated the dynamical phase transition in a system of cold atoms trapped in one-dimensional optical lattices. This is the first work to study the dynamical phase transition in a continuous model, and I have revealed the relation between the dynamical phase transition and temporal orthogonality. Third, I consider an impurity coupled to a gas in a two-dimensional lattice. This work has explored the dynamics of the impurity and proposed an approach to probe the local excitation spectrum of the gas at the site coupled to the impurity. Next, I present my contribution to a project on Bayesian estimation with continuous-variable systems. I have examined what is the best probe state for heterodyne or homodyne detection to estimate a single parameter. In the last project, I have explored steady states in quantum thermal machines. As dealing with multi-level and larger numbers of systems quickly becomes intractable, I have mapped them to lower-dimensional systems by utilising the idea of virtual qubits so that one can design autonomous quantum machines beyond a few qubits
Flow Instabilities and Vortex Dynamics in Intersecting Flows
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyFlow instabilities frequently arise in the proximity of stagnation points, often resulting in the formation of vortices. Predicting vortex formation and dynamics is important for numerous applications including engineering of bridges, airplanes and pipelines. However, vortices are intermittent in nature and it is a challenge to control and study their dynamics. Here we induce vortex formation in 4-way intersections, in which the onset of flow instability is highly sensitive to small changes of the experimental parameters (i.e., channel depth:width ratio α, fluid properties and the Reynolds number, Re). Microfluidic cross-slot geometries, with a novel configuration, are fabricated by selective laser-induced etching in fused silica glass, enabling quantitative flow velocimetry measurements at the cross-section of the intersecting region. By precisely controlling Re, the breaking of symmetry between 4-cells of Dean vortices is initiated at a critical value 10 0:55 the transition becomes hysteretic. By adjusting α and imposing Re >> Rec, we can control the nature of periodic fluctuations which are governed by the central vortex core structure and the presence of side vortices in the surrounding flow field. Additionally, we find that a slight increase of the elasticity of the fluid, by introducing small quantities of flexible polymers, destabilizes the flow, resulting in symmetry breaking at reduced Rec. We also find that the polymer torque acts counter to the vorticity, reducing the vortex intensity. Our experiments show that by tuning α, Reand elasticity we gain precise control over the intensity, core structure, dynamics and periodic fluctuations of the vortical flow field at the intersection. These experiments capture fundamental processes that govern flow transitions and provide important insights into the mechanisms of symmetry breaking, vortex dynamics and of turbulent drag reduction by polymers. Our findings contribute to the improvement of flow control and advancement of applicable technologies in which vortex suppression is required (i.e., stabilization of structures), or when vortex induced motion is desired (i.e., energy harvesting, mixing enhancement) and are transferable to systems with similar flow behavior (i.e., Taylor-Couette apparatus, T-channels, flows around cylinders and at the wake of airplane wings)
Imaging Monopoles in Spin Ice via Electron Holography
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyOriginally proposed by Pierre Curie, magnetic monopoles in vacuum have long remained elusive to detection, but recently mergent monopoles of the microscopic H field have been shown to exist in spin ice. As such, they present a valuable testing ground for the physics of magnetic monopoles which remain elusive as high energy particles. However, signatures of monopoles in spin-ice materials have only been indirect so far, and their direct observation has remained an open challenge since their discovery. One such technique that would make this direct observation a reality is electron holography, due to the electron’s high sensitivity to magnetic fields via the Aharonov-Bohm effect. Currently the best holographic microscopes can achieve 3D spatial imaging of spin phenomena with sub-nanometer resolution. In this thesis, I explore the possibility of imaging monopoles with electron holography through experimental measurements of monopole and spin ice analogs and computational simulation of how a monopole would appear in a pyrochlore spin ice thin film. My experimental work focused on measuring the phase signal from an elongated magnetic needle, as well as artificial spin ice formed from a 2D lattice of nanoscale magnets. My simulated results show for the first time what a monopole in pyrochlore spin ice would look like if imaged using electron holography. The experimental and simulation results together help define the technical requirements and experimental signals required to achieve direct observation of magnetic monopoles in spin ice via electron holography
Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica
Get PDFOikopleura dioica is a planktonic chordate with exceptional filter-feeding ability, rapid generation time, conserved early development, and a compact genome. For these reasons, it is considered a useful model organism for marine ecological studies, evolutionary developmental biology, and genomics. As research often requires a steady supply of animal resources, it is useful to establish a reliable, low-maintenance culture system. Here we describe a step-by-step method for establishing an O. dioica culture. We describe how to select potential sampling sites, collection methods, target animal identification, and the set-up of the culturing system. We provide troubleshooting advice based on our own experiences. We also highlight critical factors that help sustain a robust culture system. Although the culture protocol provided here is optimized for O. dioica, we hope our sampling technique and culture setup will inspire new ideas for maintaining other fragile pelagic invertebrates.journal articl
Spatiotemporally tracking of nano-biofilaments inside the nuclear pore complex core
Get PDFNuclear pore complex (NPC) is a gating nanomachine with a central selective barrier composed mainly of Nups, which contain intrinsically disordered (non-structured) regions (IDRs) with phenylalanine-glycine (FG) motifs (FG-NUPs). The NPC central FG network dynamics is poorly understood, as FG-NUPs liquid-liquid phase separation (LLPS) have evaded structural characterization. Moreover, the working mechanism of single FG-NUP-biofilaments residing at the central lumen is unknown. In general, flexible biofilaments are expected to be tangled and knotted during their motion and interaction. However, filament knotting visualization in real-time and space has yet to be visualized at the nanoscale. Here, we report a spatiotemporally tracking method for FG-NUP organization with nanoscale resolution, unveiling FG-NUP conformation in NPCs of colorectal cells and organoids at timescales of ~150 ms using high-speed atomic force microscopy (HS-AFM). Tracking of FG-NUP single filaments revealed that single filaments have a heterogeneous thickness in normal and cancer models which in turn affected the filament rotation and motion. Notably, FG-NUPs are overexpressed in various cancers. Using the FG-NUP inhibitor, trans-1,2-cyclohexanediol, we found that central plug size was significantly reduced and incompletely reversible back to filamentous structures in aggressive colon cancer cells and organoids. These data showed a model of FG-NUPs reversible self-assembly devolving into the central plug partial biogenesis. Taken together, HS-AFM enabled the tracking and manipulation of single filaments of native FG-NUPs which has remained evasive for decades.journal articl
Intermittent percolation and the scale-free distribution of vegetation clusters
Get PDFUnderstanding the causes and effects of spatial vegetation patterns is a fundamental problem in ecology, especially because these can be used as early predictors of catastrophic shifts such as desertification processes. Empirical studies of the vegetation cover in some areas such as drylands and semiarid regions have revealed the existence of vegetation patches of broadly diverse sizes. In particular, the probability distribution of patch sizes can be fitted by a power law, i.e. vegetation patches are approximately scale free up to some maximum size. Different explanatory mechanisms, such as plant–plant interactions and plant-water feedback loops have been proposed to rationalize the emergence of such scale-free patterns, yet a full understanding has not been reached. Using a simple model for vegetation dynamics, we show that environmental temporal variability—a well-recognized feature of semiarid environments—promotes in a robust way (i.e. for a wide range of parameter values) the emergence of vegetation patches with broadly distributed cluster sizes. Furthermore, this result is related to a percolation phenomenon that occurs in an intermittent or fluctuating way. The model also reveals that the power-law exponents fitting the tails of the probability distributions depend on the overall vegetation-cover density, in agreement with empirical observations. This supports the idea that environmental variability plays a key role in the formation of scale-free vegetation patterns. From a practical viewpoint, this may be of importance to predict the effects that changes in environmental conditions may have in real ecosystems. From a theoretical side, our study sheds new light on a novel type of percolation phenomena occurring under temporally-varying external conditions, that still needs further work to be fully characterized.journal articl
Revealing the structure of information flows discriminates similar animal social behaviors
Get PDFBehavioral correlations stretching over time are an essential but often neglected aspect of interactions among animals. These correlations pose a challenge to current behavioral-analysis methods that lack effective means to analyze complex series of interactions. Here we show that non-invasive information-theoretic tools can be used to reveal communication protocols that guide complex social interactions by measuring simultaneous flows of different types of information between subjects. We demonstrate this approach by showing that the tandem-running behavior of the ant Temnothorax rugatulus and that of the termites Coptotermes formosanus and Reticulitermes speratus are governed by different communication protocols. Our discovery reconciles the diverse ultimate causes of tandem running across these two taxa with their apparently similar signaling mechanisms. We show that bidirectional flow of information is present only in ants and is consistent with the use of acknowledgement signals to regulate the flow of directional information.journal articl
Development of 19 universal microsatellite loci for three closely related Ficus species (Moraceae) by high-throughput sequencing
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Fracton States of Matter: From Holography to Frustrated Magnetism
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe discipline of modern condensed matter physic has a lot ambitions: to discover all possible quantum phases of matter, to study the exotic properties and applications of different matter states, and to realize them in experiments. A recent exciting development in this field is the discovery of the fracton states of matter. Featuring immobile excitations and gauged/ungauged subsystem symmetries, it is a phase of quantum many-body systems that transcend the traditional scenarios of Landau-Ginsberg symmetry breaking and topological quantum states. This thesis is devoted to a few aspects of the fracton states of matter. First, we study a unique property of the fracton models: they mimic the quantum-informational features of gravity. This can be shown in the context of holographic principle or AdS/CFT duality: a fracton model in AdS space can be shown to satisfy the major properties of holography: the boundary entanglement entropy satisfies Ryu-Takayanagi formula, and the bulk reconstruction follows the Rindler reconstruction. Furthermore, the fracton model in hyperbolic space is known to be similar to various other toy models of holography including holographic tensor-networks and bit-threads model. The intriguing similarity between fracton models and gravity, as well as its implications, are discussed at length. In the second half of the thesis, we explore possible experimental routes to realize the fraction phases. Here we focus on frustrated magnets on the pyrochlore lattice, one of the most versatile and experimentally fruitful framework to realize spin liquids. By analyzing the symmetry and the coarse-grained limit of the model, we find it possible to realize various versions of rank-2 U(1) gauge theory, and some of them are simple enough to be experimentally realistic. We also propose ways to introduce quantum dynamics via frustration of higher spins