arXiv subjects

Teruaki Okushima

Publications and source records attributed to Teruaki Okushima.

7 recordsLinked to original sources

arXiv2019

Mean first passage times reconstruct the slowest relaxations in potential energy landscapes of nanoclusters

Relaxation modes are the collective modes in which all probability deviations from equilibrium states decay with the same relaxation rates. In contrast, a first passage time is the required time for arriving for the first time from one state to another. In this paper, we discuss how and why the slowest relaxation rates of relaxation modes are reconstructed from the first passage times. As an illustrative model, we use a continuous-time Markov state model of vacancy diffusion in KCl nanoclusters. Using this model, we reveal that all characteristics of the relaxations in KCl nanoclusters come from the fact that they are hybrids of two kinetically different regions of the fast surface and slow bulk diffusions. The origin of the different diffusivities turns out to come from the heterogeneity of the activation energies on the potential energy landscapes. We also develop a stationary population method to compute the mean first passage times as mean times required for pair annihilations of particle-hole pairs, which enables us to obtain the symmetric results of relaxation rates under the exchange of the sinks and the sources. With this symmetric method, we finally show why the slowest relaxation times can be reconstructed from the mean first passage times.

physics.atm-clus↗

arXiv2018

Changes of graph structure of transition probability matrices indicate the slowest kinetic relaxations

Graphs of the most probable transitions for a transition probability matrix, $e^{τK}$, i.e., the time evolution matrix of the transition rate matrix $K$ over a finite time interval $τ$, are considered. We study how the graph structures of the most probable transitions change as functions of $τ$, thereby elucidating that a kinetic threshold $τ_g$ for the graph structures exists. Namely, for $τ<τ_g$, the number of connected graph components are constant. In contrast, for $τ\geq τ_g$, recombinations of most probable transitions over the connected graph components occur multiple times, which introduce drastic changes into the graph structures. Using an illustrative multi-funnel model, we show that the recombination patterns indicate the existence of the eigenvalues and eigenvectors of slowest relaxation modes quite precisely. We also devise an evaluation formula that enables us to correct the values of eigenvalues with high accuracy from the data of merging processes. We show that the graph-based method is valid for a wide range of kinetic systems with degenerate, as well as non-degenerate, relaxation rates.

cond-mat.dis-nn↗

arXiv2018

Slowest kinetic modes revealed by metabasin renormalization

Understanding the slowest relaxations of complex systems, such as relaxation of glass-forming materials, diffusion in nanoclusters, and folding of biomolecules, is important for physics, chemistry, and biology. For a kinetic system, the relaxation modes are determined by diagonalizing its transition rate matrix. However, for realistic systems of interest, numerical diagonalization, as well as extracting physical understanding from the diagonalization results, is difficult due to the high dimensionality. Here, we develop an alternative and generally applicable method of extracting the long-time scale relaxation dynamics by combining the metabasin analysis of Okushima et al. [Phys. Rev. E 80, 036112 (2009)] and a Jacobi method. We test the method on a illustrative model of a four-funnel model, for which we obtain a renormalized kinematic equation of much lower dimension sufficient for determining slow relaxation modes precisely. The method is successfully applied to the vacancy transport problem in ionic nanoparticles [Niiyama et al. Chem. Phys. Lett. 654, 52 (2016)], allowing a clear physical interpretation that the final relaxation consists of two successive, characteristic processes.

cond-mat.mes-hall↗

arXiv2015

Instanton-noninstanton transition in nonintegrable tunneling processes: A renormalized perturbation approach

The instanton-noninstanton (I-NI) transition in the tunneling process, which has been numerically observed in classically nonintegrable quantum maps, can be described by a perturbation theory based on an integrable Hamiltonian renormalized so as to incorporate the integrable part of the map. The renormalized perturbation theory is successfully applied to the two quantum maps, the Hénon and standard maps. In spite of different nature of tunneling in the two systems, the I-NI transition exhibits very common characteristics. In particular, the manifestation of I-NI transition is obviously explained by a remarkable quenching of the renormalized transition matrix element. The enhancement of tunneling probability after the transition can be understood as a sudden change of the tunneling mechanism from the instanton to quite a different mechanism supported by classical flows just outside of the stable-unstable manifolds of the saddle on the top of the potential barrier.

nlin.CD↗

arXiv2012

DNA as a one-dimensional chiral material. II. Dynamics of the structural transition between B form and Z form

We analyze the dynamics of structural transitions between normal right-handed B form and unusual left-handed Z form for a linear DNA molecule. The dynamics under the external torque in physiological buffer is modeled by a Langevin equation, with the potential term given by the authors previously [Phys. Rev. E 84, 021926 (2011)]. With this model, we first simulate the relaxation processes around B-form structure after sudden changes of the external torques, where slow relaxation $\sim t^{-1/2}$ as a function of the elapsed time $t$ is observed. Then, the dynamics of structural transition from Z form to B form is computed under various external torque strength. For small external torques, the transition proceeds via nucleation and the growth, while for higher torques, Z-form structure becomes unstable, and the transition mechanism is switched to a spinodal-like process. These numerical results are qualitatively understood by simple phenomenological arguments.

q-bio.BM↗

arXiv2011

DNA as a one-dimensional chiral material: Application to the structural transition between B form and Z form

A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration together with a gauge principle. Motivated by a recent experiment reporting chiral transitions between right-handed B-DNA and left-handed Z-DNA [M. Lee, et. al., Proc. Natl. Acad. Sci. (USA) 107, 4985 (2010)], we analyze the free energy for the particular case of linear DNA with an externally applied torque. The model shows that there exists, at low temperature, a rapid structural change depending on the torque exerted on the DNA, which causes switching in B and Z domain sizes. This can explain the frequent switches of DNA extension observed in experiments.

physics.bio-ph↗

arXiv1998

Quantum Optics in Dispersive and Absorptive Media

Using microscopic models in which both photons and excitons are treated as microscopic degrees of freedom, we discuss polaritons of two cases: One is the case when excitonic parameters are time dependent. The time dependence causes creation of polaritons from a "false vacuum." % We present the creation spectra of both % the lower- and upper-branch polaritons. It is shown that both the creation sepctra and the creation efficiency are much different from the results of the previous studies. The other is polaritons in absorptive and inhomogeneous cavities. A polariton in such a system cannot be viewed as a back and forth oscillation between a photon state and an exciton state.

quant-ph↗