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Takenobu Nakamura

Publications and source records attributed to Takenobu Nakamura.

17 recordsLinked to original sources

Gibbs Factorials Become Kinetic in History-Dependent Reactions

Gibbs factorials are usually regarded as equilibrium counting factors. We show that they can also appear directly in a measurable kinetic observable when products formed at different stages are statistically distinguished in the history ensemble. In a model designed to isolate the essential ingredients, transient AB$_2$ complexes are stabilized as C molecules either in a single operation or through a two-stage procedure. The mean-waiting-time ratio is governed by a kinetic advantage factor $\mathcal{A}_C$ defined from equilibrium probabilities. A fluctuation-theorem argument identifies the dominant contribution $n_{\mathrm C}!/[n_{\mathrm m}!(n_{\mathrm C}-n_{\mathrm m})!]$, where $n_{\mathrm m}$ is the intermediate product number and $n_{\mathrm C}$ is the final target. This Gibbs factorial arises because products formed before and after the intermediate operation are statistically distinguished in the history ensemble, although the final molecules are macroscopically identical. Molecular dynamics simulations confirm the predicted combinatorial scaling of the mean-waiting-time ratio.

cond-mat.stat-mech↗

Probing Anharmonic and Heterogeneous Carrier Dynamics Across Sublattice Melting in a Minimal Model Superionic Conductor

Despite decades of research, the microscopic origin of sublattice melting and fast ion transport in superionic conductors remains elusive. Here, we introduce a chemically neutral minimal binary model consisting of a rigid host lattice stabilized by short-range steric repulsion and a soft carrier sublattice interacting via long-range Wigner-type forces. This contrast naturally produces distinct melting temperatures and an intermediate sublattice-melting phase in which carriers become fluidlike while the host remains crystalline. Molecular dynamics simulations identify three dynamical regimes-crystalline, sublattice-melt, and fully molten-marked by sharp changes in diffusivity, structural correlations, and dynamical heterogeneity. Near sublattice melting, carrier motion is strongly anharmonic and spatially heterogeneous, beyond mean-field hopping descriptions. By tuning the density, we demonstrate that sublattice melting can be continuously controlled, establishing a direct link between lattice softness, anharmonicity, and collective ion transport. Comparison with conventional long-range Coulombic models confirms that our minimal model reproduces the key dynamical signatures of superionicity, providing a unified microscopic foundation for designing mechanically robust superionic conductors.

cond-mat.soft↗

Persistent homology elucidates hierarchical structures responsible for mechanical properties in covalent amorphous solids

Understanding how atomic-level structures govern the mechanical properties of amorphous materials remains a fundamental challenge in solid-state physics. Under mechanical loading, amorphous materials exhibit simple affine and spatially inhomogeneous nonaffine displacements that contribute to the elastic modulus through the Born (affine) and nonaffine terms, respectively. The differences between soft local structures characterized by small Born terms or large nonaffine displacements have yet to be elucidated. This challenge is particularly complex in covalent amorphous materials such as silicon, where the medium-range order (MRO) plays a crucial role in the network structure. To address these issues, we combined molecular dynamics simulations with persistent homology analysis. Our results reveal that local structures with small Born terms are governed by short-range characteristics, whereas those with large nonaffine displacements exhibit hierarchical structures in which short-range disorder is embedded within the MRO. These hierarchical structures are also strongly correlated with low-energy localized vibrational excitations. Our findings demonstrate that the mechanical responses and dynamic properties of covalent amorphous materials are intrinsically linked to the MRO, providing a new framework for understanding and tailoring their properties.

cond-mat.mtrl-sci↗

Persistent Homology Reveals the Role of Stiffness in Forming Topological Glasses in Dense Solutions of Ring Polymers

Ring polymers are characterized by topology-specific entanglements called threadings. In the limit of large rings, it is conjectured that a "topological glass" should emerge due to the proliferation of threadings. In this study, we used persistent homology to quantify threading structures of ring polymers with different chain stiffness and elucidate mechanisms behind topological glasses. Using coordination data from coarse-grained molecular dynamics simulations, we analyzed the topology of the union of virtual spheres centered on each monomer or center of mass. As the radius of each sphere increases, the corresponding points connect, giving rise to topological entities such as edges, loops, and facets. We then analyzed how the number of loops per ring chain and penetrated loops varies with sphere radius, focusing on the effects of chain stiffness and density. The results reveal that loops are larger in stiff ring chains, whereas flexible ring chains do not generate sufficiently large loops to establish a threading structure. The stiffness of ring polymer plays a significant role in the formation of topological glasses in ring polymers.

cond-mat.soft↗

Derivation of the Invariant Free-Energy Landscape Based on Langevin Dynamics

Conventionally defined free-energy landscape (FEL) exhibits unphysical dependence on the choice of reaction coordinates and hence lacks universal predictive ability. We here show that three physically plausible requirements uniquely determine the FEL formula for a given reaction coordinate. Our FEL is expressed solely in terms of quantities obtained through time-series data analysis, namely, the probability distribution and the diffusion matrix. It is free from any unphysical coordinate dependence and coincides with the conventional FEL in special cases. The uniqueness and robustness of the formula strongly suggest that our FEL has universal predictive power.

cond-mat.stat-mech↗

Reproducing Reaction Route Map on the Shape Space from its Quotient by Complete Nuclear Permutation-Inversion group

This study develops an algorithm to reproduce reaction route maps (RRMs) in shape space from the outputs of potential search algorithms. To demonstrate this, GRRM is utilized as a potential search algorithm but the proposed algorithm should work with other potential search algorithms in principle. The proposed algorithm does not require any encoding of the molecular configurations and is thus applicable to complicated realistic molecules for which efficient encoding is not readily available. We show subgraphs of a RRM mapped to each other by the action of the symmetry group are isomorphic and also provide an algorithm to compute the set of feasible transformations in the sense of Longuet--Higgins. We demonstrate the proposed algorithm in toy models and in more realistic molecules. Finally, we remark on absolute rate theory from our perspective.

physics.chem-ph↗

Characterizing Reaction Route Map of Realistic Molecular Reactions based on Weight Rank Clique Filtration of Persistent Homology

A reaction route map (RRM) constructed using the GRRM program is a collection of elementary reaction pathways, each of which comprises two equilibrium (EQ) geometries and one transition state (TS) geometry connected by an intrinsic reaction coordinate (IRC). An RRM can be mathematically represented by a graph with weights assigned to both vertices, corresponding to EQs, and edges, corresponding to TSs, representing the corresponding energies. In this study, we propose a method to extract topological descriptors of a weighted graph representing an RRM based on persistent homology (PH). The work of Mirth et al. [J. Chem. Phys. 2021, 154, 114114], in which PH analysis was applied to the (3N-6)-dimensional potential energy surface of an N atomic system, is related to the present method, but our method is practically applicable to realistic molecular reactions. Numerical assessments revealed that our method can extract the same information as the method proposed by Mirth et al. for the 0-th and 1-st PHs, except for the death of the 1-st PH. In addition, the information obtained from the 0-th PH corresponds to the analysis using the disconnectivity graph. The results of this study suggest that the descriptors obtained using the proposed method accurately reflect the characteristics of the chemical reactions and/or physicochemical properties of the system.

physics.chem-ph↗

Persistent Homology Analysis for Materials Research and Persistent Homology Software: HomCloud

This paper introduces persistent homology, which is a powerful tool to characterize the shape of data using the mathematical concept of topology. We explain the fundamental idea of persistent homology from scratch using some examples. We also review some applications of persistent homology to materials researches and software for persistent homology data analysis. HomCloud, one of persistent homology software, is especially featured in this paper.

math.AT↗

Persistence Homology Of Entangled Rings

Topological constraints (TCs) between polymers determine the behaviour of complex fluids such as creams, oils and plastics. Most of the polymer solutions used every day life employ linear chains; their behaviour is accurately captured by the reptation and tube theories which connect microscopic TCs to macroscopic viscoelasticity. On the other hand, polymers with non-trivial topology, such as rings, hold great promise for new technology but pose a challenging problem as they do not obey standard theories; additionally, topological invariance -- i.e. the fact that rings must remain unknotted and unlinked if prepared so -- precludes any serious analytical treatment. Here we propose an unambiguous, parameter-free algorithm to characterise TCs in polymeric solutions and show its power in characterising TCs of entnagled rings. We analyse large-scale molecular dynamics (MD) simulations via persistent homology, a key mathematical tool to extract robust topological information from large datasets. This method allows us to identify ring-specific TCs which we call "homological threadings" (H-threadings) and to connect them to the polymers' behaviour. It also allows us to identify, in a physically appealing and unambiguous way, scale-dependent loops which have eluded precise quantification so far. We discover that while threaded neighbours slowly grow with the rings' length, the ensuing TCs are extensive also in the asymptotic limit. Our proposed method is not restricted to ring polymers and can find broader applications for the study of TCs in generic polymeric materials.

cond-mat.soft↗

Microscopic Description of Yielding in Glass Based on Persistent Homology

Persistent homology (PH) was applied to probe the structural changes of glasses under shear. PH associates each local atomistic structure in an atomistic configuration to a geometric object, namely, a hole, and evaluates the robustness of these holes against noise. We found that the microscopic structures were qualitatively different before and after yielding. The structures before yielding contained robust holes, the number of which decreased after yielding. We also observed that the structures after yielding approached those of quickly quenched glass. This work demonstrates the crucial role of robust holes in yielding and provides an interpretation based on geometry.

cond-mat.stat-mech↗

Hierarchical structures of amorphous solids characterized by persistent homology

This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the PDs is given by an atomic configuration and the output is expressed as 2D histograms. Then, specific distributions such as curves and islands in the PDs identify meaningful shape characteristics of the atomic configuration. Although the method can be applied to a wide variety of disordered systems, it is applied here to silica glass, the Lennard-Jones system, and Cu-Zr metallic glass as standard examples of continuous random network and random packing structures. In silica glass, the method classified the atomic rings as short-range and medium-range orders and unveiled hierarchical ring structures among them. These detailed geometric characterizations clarified a real space origin of the first sharp diffraction peak and also indicated that PDs contain information on elastic response. Even in the Lennard-Jones system and Cu-Zr metallic glass, the hierarchical structures in the atomic configurations were derived in a similar way using PDs, although the glass structures and properties substantially differ from silica glass. These results suggest that the PDs provide a unified method that extracts greater depth of geometric information in amorphous solids than conventional methods.

cond-mat.soft↗

Persistent Homology and Many-Body Atomic Structure for Medium-Range Order in the Glass

Characterization of medium-range order in amorphous materials and its relation to short-range order is discussed. A new topological approach is presented here to extract a hierarchical structure of amorphous materials, which is robust against small perturbations and allows us to distinguish it from periodic or random configurations. The method is called the persistence diagram (PD) and it introduces scales into many-body atomic structures in order to characterize the size and shape. We first illustrate how perfect crystalline and random structures are represented in the PDs. Then, the medium-range order in the amorphous silica is characterized by using the PD. The PD approach reduces the size of the data tremendously to much smaller geometrical summaries and has a huge potential to be applied to broader areas including complex molecular liquid, granular materials, and metallic glasses.

cond-mat.soft↗

Derivation of the nonlinear fluctuating hydrodynamic equation from underdamped Langevin equation

We derive the fluctuating hydrodynamic equation for the number and momentum densities exactly from the underdamped Langevin equation. This derivation is an extension of the Kawasaki-Dean formula in underdamped case. The steady state probability distribution of the number and momentum densities field can be expressed by the kinetic and potential energies. In the massless limit, the obtained fluctuating hydrodynamic equation reduces to the Kawasaki-Dean equation. Moreover, the derived equation corresponds to the field equation derived from the canonical equation when the friction coefficient is zero.

cond-mat.stat-mech↗

A fluctuation-response relation of many Brownian particles under non-equilibrium conditions

We study many interacting Brownian particles under a tilted periodic potential. We numerically measure the linear response coefficient of the density field by applying a slowly varying potential transversal to the tilted direction. In equilibrium cases, the linear response coefficient is related to the intensity of density fluctuations in a universal manner, which is called a fluctuation-response relation. We then report numerical evidence that this relation holds even in non-equilibrium cases. This result suggests that Einstein's formula on density fluctuations can be extended to driven diffusive systems when the slowly varying potential is applied in a direction transversal to the driving force.

cond-mat.stat-mech↗

Experimental Test of a New Equality: Measuring Heat Dissipation in an Optically Driven Colloidal System

Measurement of energy dissipation in small nonequilibrium systems is generally a difficult task. Recently, Harada and Sasa [Phys.Rev.Lett. 95, 130602(2005)] derived an equality relating the energy dissipation rate to experimentally accessible quantities in nonequilibrium steady states described by the Langevin equation. Here, we show the first experimental test of this new relation in an optically driven colloidal system. We find that this equality is validated to a fairly good extent, thus the irreversible work of a small system is estimated from readily obtainable quantities.

cond-mat.stat-mech↗

Systematic derivation of coarse-grained fluctuating hydrodynamic equations for many Brownian particles under non-equilibrium condition

We study the statistical properties of many Brownian particles under the We study the statistical properties of many Brownian particles under the influence of both a spatially homogeneous driving force and a periodic potential with period $\ell$ in a two-dimensional space. In particular, we focus on two asymptotic cases, $\ell_{\rm int} \ll \ell$ and $\ell_{\rm int} \gg \ell$, where $\ell_{\rm int}$ represents the interaction length between two particles. We derive fluctuating hydrodynamic equations describing the evolution of a coarse-grained density field defined on scales much larger than $\ell$ for both the cases. Using the obtained equations, we calculate the equal-time correlation functions of the density field to the lowest order of the interaction strength. We find that the system exhibits the long-range correlation of the type $r^{-d}$ ($d=2$) for the case $\ell_{\rm int} \gg \ell$, while no such behavior is observed for the case $\ell_{\rm int}\ll \ell$.

cond-mat.stat-mech↗

Anomalous time correlation in two-dimensional driven diffusive systems

We study the time correlation function of a density field in two-dimensional driven diffusive systems within the framework of fluctuating hydrodynamics. It is found that the time correlation exhibits power-law behavior in an intermediate time regime in the case that the fluctuation-dissipation relation is violated and that the power-law exponent depends on the extent of this violation. We obtain this result by employing a renormalization group method to treat a logarithmic divergence in time.

cond-mat.stat-mech↗