arXiv subjects

Masaki Kato

Publications and source records attributed to Masaki Kato.

11 recordsLinked to original sources

arXiv2025

QBIOL: A quantum bioelectrochemical software based on point stochastic processes

Bioelectrochemistry is crucial for understanding biological functions and driving applications in synthetic biology, healthcare, and catalysis. However, current simulation methods fail to capture both the stochastic nature of molecular motion and electron transfer across the relevant picosecond-to-minute timescales. We present QBIOL, a web-accessible software that integrates molecular dynamics, applied mathematics, GPU programming, and quantum charge transport to address this challenge. QBIOL enables quantitative stochastic electron transfer simulations and has the potential to reproduce numerically any (bio) electrochemical experiments. We illustrate this potential by comparing our simulations with experimental data on the current generated by electrode-attached redox-labeled DNA, or by nanoconfined redox species, in response to a variety of electrical excitation waveforms, configurations of interest in biosensing and catalysis. The adaptable architecture of QBIOL extends to the development of devices for quantum and molecular technologies, positioning our software as a powerful tool for enabling new research in this rapidly evolving field.

cond-mat.mes-hall↗

arXiv2025

Symmetry requirements for current-induced spin magnetization specific to chiral crystals: Multipole analysis and the hidden spin glide symmetry

Current-induced spin magnetization (CISM) specific to chiral crystals is microscopically analyzed using multipole theory to identify the necessary hopping and spin-orbit couplings (SOCs). Tight-binding models capturing the essence of chiral crystals are introduced to investigate the multipole degrees of freedom possessed by the Hamiltonian. The results reveal that chiral SOC has a multipole degree of freedom specific to chiral crystals. Subsequently, the CISM is evaluated numerically and analytically. The results show that in addition to the chiral SOC, hopping along the $z$-axis, which is irrelevant from a multipole perspective, is crucial for CISM. This hopping is required to break the combined symmetry of wavevector translation and spin flipping, which we refer to as spin glide symmetry. This confirms that hopping irrelevant to chirality can play a crucial role in physical properties arising from chirality without contradicting the framework of multipole theory.

cond-mat.mes-hall↗

arXiv2025

Optimality theory of stigmergic collective information processing by chemotactic cells

Collective information processing is fundamental in various biological systems, where the cooperation of multiple cells results in complex functions beyond individual capabilities. A distinctive example is collective exploration where chemotactic cells not only sense the gradient of guiding exogeneous cues originating from targets but also generate and modulate endogenous cues to coordinate their collective behaviors. While the optimality of gradient sensing has been studied extensively in the context of single-cell information processing, the optimality of collective information processing that includes both gradient sensing and gradient generation remains underexplored. In this study, we formulate the collective exploration problem as a reinforcement learning (RL) by a population. Based on RL theory, we derive the optimal exploration dynamics of agents and identify their structural correspondence with the Keller-Segel model, the established phenomenological model of collective cellular dynamics. Our theory identifies an optimal coupling relation between gradient sensing and gradient generation and demonstrates that the optimal way to generate a gradient qualitatively differs depending on whether the gradient sensing is logarithmic or linear. The underlying RL structure is leveraged to compare the derived collective dynamics with single-agent searching dynamics, showing that distributed information processing by population enables a fraction of agents to reach the target robustly. Our formulation provides a foundation for understanding the collective information processing mediated by dynamic sensing and modulation of cues.

q-bio.CB↗

arXiv2024

Phase diagram of pressure-induced high temperature superconductor La$_{3}$Ni$_{2}$O$_{7+δ}$

We successfully synthesized samples of La$_{3}$Ni$_{2}$O$_{7+δ}$ ($δ= -0.50$, $-0.16$, $0.00$, $+0.01$, and $+0.12$) and measured the resistance under extremely high pressures using a diamond anvil cell to establish the electronic phase diagram. A Mott insulating state appears at $δ= -0.50$, where all Ni ions are divalent. With increasing oxygen content, superconductivity appears at $δ= 0.00$ and higher, above approximately 25 GPa, passing through Anderson localization at $δ= -0.16$. The superconducting transition temperature $T_{\mathrm{c}}$ decreases with increasing pressures for both $δ= 0.00$ and $+0.12$, with the pressure dependence of $T_{\mathrm{c}}$ being much stronger in the latter than in the former.

cond-mat.supr-con↗

arXiv2024

Pressure-induced superconductivity in La$_{4}$Ni$_{3}$O$_{10+δ}$ ($δ$ = 0.04 and -0.01)

The superconducting transition temperatures, $T_{\mathrm{c}}$, of La$_{4}$Ni$_{3}$O$_{10+δ}$($δ$ = 0.04 and -0.01) were determined under various pressures up to 124.9 GPa by electrical resistance measurements with a diamond anvil cell. $T_{\mathrm{c}}$ exhibits a strong dependence on oxygen content within the pressure range of approximately 20 GPa and 80 GPa. At 48.0 GPa, $T_{\mathrm{c}}$ of La$_{4}$Ni$_{3}$O$_{10.04}$ peaks at 36 K, marking the highest $T_{\mathrm{c}}$ reported thus far.

cond-mat.supr-con↗

arXiv2024

Interatomic spin-orbit coupling in atomic orbital-based tight-binding models

Interatomic hopping mediated by spin-orbit coupling (SOC) entangles spin, orbital and sublattice degrees of freedom of electrons, leading to the emergence of intriguing phenomena such as novel topological insulators and exotic spin-dependent transport including chirality-induced spin selectivity (CISS). Despite these effects, a comprehensive microscopic formalism to describe the spin-dependent hopping remains insufficiently established. In this study, we systematically investigate SOC hopping by analytically deriving the hopping integrals within a two-center approximation based on atomic orbitals. Introducing independent parameters, or extended Slater-Koster symbols, that characterize SOC hopping, we explicitly determine the form of the hopping for $s$, $p$ and $d$ orbitals in the arbitrary hopping directions. Our formalism is then implemented in tight-binding models on several lattices. Furthermore, we examine the effect of SOC on band dispersion by employing a multipole decomposition for the SOC Hamiltonian, providing a fundamental understanding of SOC-induced phenomena. In particular, we derive an explicit expression for the SOC Hamiltonian that causes unique spin splitting in chiral systems by considering a triangular helical chain. Most importantly, the obtained SOC Hamiltonian does not contain a term that has the symmetry of electric toroidal monopole $G_0$ but rather an electric toroidal quadrupole $G_u$, which is the origin of chirality in this case.

cond-mat.mtrl-sci↗

arXiv2024

Theoretical analysis on the possibility of superconductivity in a trilayer Ruddlesden-Popper nickelate La$_4$Ni$_3$O$_{10}$ under pressure and its experimental examination: comparison with La$_3$Ni$_2$O$_7$

We study the possibility of superconductivity in a trilayer Ruddlesden-Popper nickelate La$_4$Ni$_3$O$_{10}$ under pressure both theoretically and experimentally, making comparison with the recently discovered high $T_c$ superconductor La$_3$Ni$_2$O$_7$, a bilayer nickelate. Through DFT calculations, we find that a structural phase transition from monoclinic to tetragonal takes place around 10 - 15 GPa. Using the tetragonal crystal structure, we theoretically investigate the possibility of superconductivity, where a combination of fluctuation exchange approximation and linearized Eliashberg equation is applied to a six-orbital model constructed from first principles band calculation. The obtained results suggests that La$_4$Ni$_3$O$_{10}$ may also become superconducting under high pressure with $T_c$ comparable to some cuprates, although it is not as high as La$_3$Ni$_2$O$_7$. We also perform experimental studies using our polycrystalline samples of La$_3$Ni$_2$O$_{7.01}$ and La$_4$Ni$_3$O$_{9.99}$. The superconducting transition of La$_3$Ni$_2$O$_{7.01}$, with a maximum onset $T_c$ of 67.0 K at a pressure of 26.5 GPa, is confirmed by a drop in the electrical resistance, as well as the magnetic field dependence of the resistance. Quite interestingly, similar temperature and magnetic field dependencies of the resistance are observed also for La$_4$Ni$_3$O$_{9.99}$, where a drop in the resistance is observed at lower temperatures compared to La$_3$Ni$_2$O$_{7.01}$, under pressures of 32.8 GPa and above. Given the theoretical expectation, the reduction in the resistance can most likely be attributed to the occurrence of superconductivity in La$_4$Ni$_3$O$_{9.99}$. The temperature at which the resistance deviates from a linear behavior, considered as the onset $T_c$, monotonically increases up to 23 K at 79.2 GPa, which is opposite to the pressure dependence of $T_c$ in La3Ni2O7.01.

cond-mat.supr-con↗

arXiv2024

Chirality-Induced Selectivity of Phonon Angular Momenta in Chiral Quartz Crystals

A generation, propagation, and transfer of phonon angular momenta are examined on thermal transport in chiral insulative and diamagnetic crystals of $α$-quartz. We found that thermally-driven phonons carry chirality-dependent angular momenta in the quartz crystals and they could be extracted from the quartz as a spin signal. Namely, chirality-induced selectivity of phonon angular momenta is realized in the chiral quartz. We argue that chiral phonons available in chiral materials could be a key element in triggering or enhancing chirality-induced spin selectivity with robust spin polarization and long-range spin transport found in various chiral materials.

cond-mat.mtrl-sci↗

arXiv2022

Partial synchronization and community switching in phase-oscillator networks and its analysis based on a bidirectional, weighted chain of three oscillators

Complex networks often possess communities defined based on network connectivity. When dynamics undergo in a network, one can also consider dynamical communities; i.e., a group of nodes displaying a similar dynamical process. We have investigated both analytically and numerically the development of dynamical community structure, where the community is referred to as a group of nodes synchronized in frequency, in networks of phase oscillators. We first demonstrate that using a few example networks, the community structure changes when network connectivity or interaction strength is varied. In particular, we found that community switching, i.e., a portion of oscillators change the group to which they synchronize, occurs for a range of parameters. We then propose a three-oscillator model: a bidirectional, weighted chain of three Kuramoto phase oscillators, as a theoretical framework for understanding the community formation and its variation. Our analysis demonstrates that the model shows a variety of partially synchronized patterns: oscillators with similar natural frequencies tend to synchronize for weak coupling, while tightly connected oscillators tend to synchronize for strong coupling. We obtain approximate expressions for the critical coupling strengths by employing a perturbative approach in a weak coupling regime and a geometric approach in a strong coupling regimes. Moreover, we elucidate the bifurcation types of transitions between different patterns. Our theory might be useful for understanding the development of partially synchronized patterns in a wider class of complex networks than community structured networks.

nlin.AO↗

arXiv2022

Flux roughening in spin ice with mixed $\pm J$ interactions

Spin ice presents a typical example of classical spin liquid, where conserved magnetic fluxes emerge from microscopic spin degrees of freedom. In this letter, we investigate the effect of perturbation by magnetic charge disorder in two-dimensional spin ice. To this aim, we develop a novel cluster update algorithm, which enables fast relaxation of magnetic charges. The efficient Monte Carlo calculation reveals a drastic change of spin structure factor as doping magnetic charges: the pinch point, characterizing the spin ice, is gradually replaced by a diffusive peak. We derive an analytical relation connecting the flux fluctuation and the spin structure factor, and explain the evolution of diffusive peak in terms of the roughening of magnetic fluxes.

cond-mat.str-el↗

arXiv2021

Magnetic Switching by Oxygen Adsorption in Metal-Organic Framework Systems

In this letter, we address magnetization switching by oxygen adsorption in porous metal-organic framework systems. To this end, we construct a simple localized spin model combined with a Langmuir-type formula for oxygen adsorption and study its finite-temperature properties using Monte Carlo simulation. We successfully explain the main features of this phenomenon, such as the discontinuous changes in magnetic states, sensitivity of the magnetic transition temperatures to oxygen pressure, and absence of singularities in adsorbed oxygen. Based on this model, we also reproduce the observed magnetic transition temperatures for a typical value of oxygen adsorption energy.

cond-mat.mtrl-sci↗