arXiv subjects

Hiroki Ohta

Publications and source records attributed to Hiroki Ohta.

18 recordsLinked to original sources

arXiv2025

Measurement-Based Quantum Computation Using the Spin-1 XXZ Model with Uniaxial Anisotropy

We demonstrate that the ground state of a spin-1 $XXZ$ chain with uniaxial anisotropies, single-ion anisotropy $D$ and Ising-like anisotropy $J$, within the Haldane phase can serve as a resource state for measurement-based quantum computation implementing single-qubit gates. The gate fidelity of both elementary rotation gates and general single-qubit unitary gates composed of rotations about the $x$, $y$, and $z$ axes is evaluated, and is found to exceed 0.99 when $D$ or $J$ is appropriately tuned. Furthermore, we derive an analytic expression for the rotation-gate fidelity under the assumption that the state lies within the $\mathbb Z_2\times \mathbb Z_2$-protected Haldane phase, showing that it is determined by the postmeasurement spin-spin correlation function and the failure probability. The observed enhancement of gate fidelity in the spin-1 $XXZ$ chain originates from the strengthening of antiferromagnetic (AFM) correlations near the AFM phase, which effectively suppresses failure states.

quant-ph↗

arXiv2024

Emergence of vertical diversity under disturbance

We propose a statistical physics model of a neutral community, where each agent can represent identical plant species growing in the vertical direction with sunlight in the form of rich-get-richer competition. Disturbance added to this ecosystem, which makes an agent restart from the lowest growth level, is realized as a stochastic resetting. We show that in this model for sufficiently strong competition, vertical diversity characterized by a family of Hill numbers robustly emerges as a local maximum at intermediate disturbance.

cond-mat.stat-mech↗

arXiv2023

Integrative analysis of ATAC-seq and RNA-seq for cells infected by human T-cell leukemia virus type 1

Human T-cell leukemia virus type 1 (HTLV-1) causes adult T-cell leukemia (ATL) and HTLV-1-associated myelopathy (HAM) after a long latent period in a fraction of infected individuals. These HTLV-1-infected cells typically have phenotypes similar to that of CD4${^+}$ T cells, but the cell status is not well understood. To extract the inherent information of HTLV-1-infected CD4$^+$ cells, we integratively analyzed the ATAC-seq and RNA-seq data of infected cells. Compared to CD4${^+}$ T cells from healthy donors, we found anomalous chromatin accessibility in HTLV-1-infected CD4${^+}$ cells derived from ATL cases in terms of location and sample-to-sample fluctuations in open chromatin regions. Further, by focusing on systematically selected genes near the open chromatin regions, all the gene expressions in ATL cases were found to be distinct from those of healthy CD4$^+$ T cells. Based on a further analysis of chromatin accessibility, we detected TLL1 (Tolloid Like 1) as one of the key genes that exhibit unique gene expressions in ATL cases. A luciferase assay indicated that TLL1 has a strong regulatory effect on TGF-$β$. Overall, this study provides results about the status of HTLV-1 infected cells, which are qualitatively consistent across the different scales of chromatin accessibility, transcription, and immunophenotype.

q-bio.GN↗

arXiv2023

Emergent centrality in rank-based supplanting process

We propose a stochastic process of interacting many agents, which is inspired by rank-based supplanting dynamics commonly observed in a group of Japanese macaques. In order to characterize the breaking of permutation symmetry with respect to agents' rank in the stochastic process, we introduce a rank-dependent quantity, overlap centrality, which quantifies how often a given agent overlaps with the other agents. We give a sufficient condition in a wide class of the models such that overlap centrality shows perfect correlation in terms of the agents' rank in zero-supplanting limit. We also discuss a singularity of the correlation in the case of interaction induced by a Potts energy.

cond-mat.stat-mech↗

arXiv2022

Phase growth with heat diffusion in a stochastic lattice model

When a stable phase is adjacent to a metastable phase with a planar interface, the stable phase grows. We propose a stochastic lattice model describing the phase growth accompanying heat diffusion. The model is based on an energy-conserving Potts model with a kinetic energy term defined on a two-dimensional lattice, where each site is sparse-randomly connected in one direction and local in the other direction. For this model, we calculate the stable and metastable phases exactly using statistical mechanics. Performing numerical simulations, we measure the displacement of the interface $R(t)$. We observe the scaling relation $R(t)=L_x \bar{\mathcal{R}} (Dt/L_x^2)$, where $D$ is the thermal diffusion constant and $L_x$ is the system size between the two heat baths. The scaling function $\bar{\mathcal{R}}(z)$ shows $\bar{\mathcal{R}}(z) \simeq z^{0.5}$ for $z \ll z_c$ and $\bar{\mathcal{R}}(z) \simeq z^α$ for $z \gg z_c$, where the cross-over value $z_c$ and exponent $α$ depend on the temperatures of the baths, and $0.5\leα\le 1$. We then confirm that a deterministic phase-field model exhibits the same scaling relation. Moreover, numerical simulations of the phase-field model show that the cross-over value $\bar{\mathcal{R}}(z_c)$ approaches zero when the stable phase becomes neutral.

cond-mat.stat-mech↗

arXiv2020

Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells

The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards the genome as a string of $1$s and $0$s based on a set of peaks and calculates the Hamming distances between the strings. This algorithm with the systematically optimized set of peaks enables us to quantitatively evaluate differences between samples of hematopoietic cells and classify cell types, potentially leading to a better understanding of leukemia pathogenesis.

q-bio.GN↗

arXiv2017

Spatiotemporal expressions reflecting topological classes of repressor networks

A family of repressor networks is proposed as a simple model of gene regulatory networks. We analytically show three topological classes of the repressor networks, each of which exhibits distinctly growing complexity of spatiotemporal expressions starting from nearly homogeneous states. Further, by focusing on locally interacting cases such as chain networks, including a generalized repressilator, or feedforward(back)-loop networks, spatiotemporal expressions in the long time regime and elusive relationships between such different networks are discussed in detail.

cond-mat.stat-mech↗

arXiv2017

Deterministic extinction by mixing in cyclically competing species

We consider a cyclically competing species model on a ring with global mixing at finite rate, which corresponds to the well-known Lotka-Volterra equation in the limit of infinite mixing rate. Within a perturbation analysis of the model from the infinite mixing rate, we provide analytical evidence that extinction occurs deterministically at sufficiently large but finite values of the mixing rate for any species number $N\ge3$. Further, by focusing on the cases of rather small species numbers, we discuss numerical results concerning the trajectories toward such deterministic extinction, including global bifurcations caused by changing the mixing rate.

q-bio.PE↗

arXiv2014

Inferring the origin of an epidemic with a dynamic message-passing algorithm

We study the problem of estimating the origin of an epidemic outbreak -- given a contact network and a snapshot of epidemic spread at a certain time, determine the infection source. Finding the source is important in different contexts of computer or social networks. We assume that the epidemic spread follows the most commonly used susceptible-infected-recovered model. We introduce an inference algorithm based on dynamic message-passing equations, and we show that it leads to significant improvement of performance compared to existing approaches. Importantly, this algorithm remains efficient in the case where one knows the state of only a fraction of nodes.

physics.soc-ph↗

arXiv2014

Jamming transition in kinetically constrained models with reflection symmetry

A class of kinetically constrained models with reflection symmetry is proposed as an extension of the Fredrickson-Andersen model. It is proved that the proposed model on the square lattice exhibits a freezing transition at a non-trivial density. It is conjectured by numerical experiments that the known mechanism of the singular behaviors near the freezing transition in a previously studied model (spiral model) is not responsible for that in the proposed model.

cond-mat.stat-mech↗

arXiv2014

Fixation in cyclically competing species on a directed graph with quenched disorder

A simple model of cyclically competing species on a directed graph with quenched disorder is proposed as an extension of the rock-paper-scissors model. By assuming that the effects of loops in a directed random graph can be ignored in the thermodynamic limit, it is proved for any finite disorder that the system fixates to a frozen configuration when the species number $s$ is larger than the spatial connectivity $c$, and otherwise stays active. Nontrivial lower and upper bounds for the persistence probability of a site never changing its state are also analytically computed. The obtained bounds and numerical simulations support the existence of a phase transition as a function of disorder for $1<c_l(s)\le c <s$, with a $s$-dependent threshold of the connectivity $c_l(s)$.

cond-mat.stat-mech↗

arXiv2013

Morphology transition at depinning in a solvable model of interface growth in a random medium

We propose a simple, exactly solvable, model of interface growth in a random medium that is a variant of the zero-temperature random-field Ising model on the Cayley tree. This model is shown to have a phase diagram (critical depinning field versus disorder strength) qualitatively similar to that obtained numerically on the cubic lattice. We then introduce a specifically tailored random graph that allows an exact asymptotic analysis of the height and width of the interface. We characterize the change of morphology of the interface as a function of the disorder strength, a change that is found to take place at a multicritical point along the depinning-transition line.

cond-mat.stat-mech↗

arXiv2012

Lane formation in a lattice model for oppositely driven binary particles

Oppositely driven binary particles with repulsive interactions on the square lattice are investigated at the zero-temperature limit. Two classes of steady states related to stuck configurations and lane formations have been constructed in systematic ways under certain conditions. A mean-field type analysis carried out using a percolation problem based on the constructed steady states provides an estimation of the phase diagram, which is qualitatively consistent with numerical simulations. Further, finite size effects in terms of lane formations are discussed.

cond-mat.stat-mech↗

arXiv2010

Systematic perturbation approach for a dynamical scaling law in a kinetically constrained spin model

The dynamical behaviours of a kinetically constrained spin model (Fredrickson-Andersen model) on a Bethe lattice are investigated by a perturbation analysis that provides exact final states above the nonergodic transition point. It is observed that the time-dependent solutions of the derived dynamical systems obtained by the perturbation analysis become systematically closer to the results obtained by Monte Carlo simulations as the order of a perturbation series is increased. This systematic perturbation analysis also clarifies the existence of a dynamical scaling law, which provides a implication for a universal relation between a size scale and a time scale near the nonergodic transition.

cond-mat.stat-mech↗

arXiv2010

Multi-step relaxations in Glauber dynamics of a bond-diluted Ising model on a Bethe lattice

Glauber dynamics of a bond-diluted Ising model on a Bethe lattice (a random graph with fixed connectivity) is investigated by an approximate theory which provides exact results for equilibrium properties. The time-dependent solutions of the dynamical system derived by this method are in good agreement with the results obtained by Monte Carlo simulations in almost all situations. Furthermore, the derived dynamical system exhibits a remarkable phenomenon that the magnetization shows multi-step relaxations at intermediate time scales in a low-temperature part of the Griffiths phase without bond percolation clusters.

cond-mat.stat-mech↗

arXiv2009

A universal form of slow dynamics in zero-temperature random-field Ising model

The zero-temperature Glauber dynamics of the random-field Ising model describes various ubiquitous phenomena such as avalanches, hysteresis, and related critical phenomena. Here, for a model on a random graph with a special initial condition, we derive exactly an evolution equation for an order parameter. Through a bifurcation analysis of the obtained equation, we reveal a new class of cooperative slow dynamics with the determination of critical exponents.

cond-mat.stat-mech↗

arXiv2008

Critical phenomena in globally coupled excitable elements

Critical phenomena in globally coupled excitable elements are studied by focusing on a saddle-node bifurcation at the collective level. Critical exponents that characterize divergent fluctuations of interspike intervals near the bifurcation are calculated theoretically. The calculated values appear to be in good agreement with those determined by numerical experiments. The relevance of our results to jamming transitions is also mentioned.

cond-mat.stat-mech↗

arXiv2008

Critical fluctuations of time-dependent magnetization in a random-field Ising model

Cooperative behaviors near the disorder-induced critical point in a random field Ising model are numerically investigated by analyzing time-dependent magnetization in ordering processes from a special initial condition. We find that the intensity of fluctuations of time-dependent magnetization, $χ(t)$, attains a maximum value at a time $t=τ$ in a normal phase and that $χ(τ)$ and $τ$ exhibit divergences near the disorder-induced critical point. Furthermore, spin configurations around the time $τ$ are characterized by a length scale, which also exhibits a divergence near the critical point. We estimate the critical exponents that characterize these power-law divergences by using a finite-size scaling method.

cond-mat.stat-mech↗