arXiv subjects

Kenji Yasuoka

Publications and source records attributed to Kenji Yasuoka.

30 records · Page 2Linked to original sources

arXiv2014

Origin of $1/f$ noise transition in hydration dynamics on a lipid membrane surface

Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although the number of water molecules near the membrane fluctuates dynamically, the hydration dynamics has been veiled. Here we investigate residence statistics of water molecules on the surface of a lipid membrane using all-atom molecular dynamics simulations. We show that hydration dynamics on the lipid membrane exhibit $1/f^β$ noise with two different power-law exponents, $β_l < 1$ and $β_h > 1$. By constructing a dichotomous process for the hydration dynamics, we find that the process can be regarded as a non-Markov renewal process. The result implies that the origin of the $1/f$ noise transition in hydration dynamics on the membrane surface is a combination of a power-law distribution with cutoff of interoccurrence times of switching events and a long-term correlation between the interoccurrence times.

physics.bio-ph↗

arXiv2014

Origin of subdiffusion of water molecules on cell membrane surfaces

Water molecules play an important role in providing unique environments for biological reactions on cell membranes. It is widely believed that water molecules form bridges that connect lipid molecules and stabilize cell membranes. Using all-atom molecular dynamics simulations, we show that translational and rotational diffusion of water molecules on lipid membrane surfaces exhibit subdiffusion. Moreover, we provide evidence that both divergent mean trapping time (continuous-time random walk) and long-correlated noise (fractional Brownian motion) contribute to this subdiffusion. These results suggest that subdiffusion on cell membranes causes the water retardation, an enhancement of cell membrane stability, and a higher reaction efficiency.

physics.bio-ph↗

arXiv2013

Homogeneous Connectivity of Potential Energy Network in a Solidlike State of Water Cluster

A novel route to the exponential trapping-time distribution within a solidlike state in water clusters is described. We propose a simple homogeneous network (SHN) model to investigate dynamics on the potential energy networks of water clusters. In this model, it is shown that the trapping-time distribution in a solidlike state follows the exponential distribution, whereas the trapping-time distribution in local potential minima within the solidlike state is not exponential. To confirm the exponential trapping-time distribution in a solidlike state, we investigate water clusters, $($H${}_2$O$)_6$ and $($H${}_2$O$)_{12}$, by molecular dynamics simulations. These clusters change dynamically from solidlike to liquidlike state and vice versa. We find that the probability density functions of trapping times in a solidlike state are described by the exponential distribution whereas those of interevent times of large fluctuations in potential energy within the solidlike state follow the Weibull distributions. The results provide a clear evidence that transition dynamics between solidlike and liquidlike states in water clusters are well described by the SHN model, suggesting that the exponential trapping-time distribution within a solidlike state originates from the homogeneous connectivity in the potential energy network.

physics.chem-ph↗

arXiv2010

Phases of hot nuclear matter at subnuclear densities

Structure of hot dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We analyze nucleon distributions and nuclear shapes using two-point correlation functions and Minkowski functionals to determine the phase-separation line and to classify the phase of nuclear matter in terms of the nuclear structure. Obtained phase diagrams show that the density of the phase boundaries between the different nuclear structures decreases with increasing temperature due to the thermal expansion of nuclear matter region. The critical temperature for the phase separation is $\agt 6$ MeV for the proton fraction $x=0.5$ and $\agt 5$ MeV for $x=0.3$. Our result suggests the existence of "spongelike" phases with negative Euler characteristic in addition to the simple "pasta" phases in supernova cores until $T \alt 3$ MeV.

nucl-th↗

arXiv2010

Phase diagram of nuclear "pasta" and its uncertainties in supernova cores

We examine the model dependence of the phase diagram of inhomogeneous nulcear matter in supernova cores using the quantum molecular dynamics (QMD). Inhomogeneous matter includes crystallized matter with nonspherical nuclei - "pasta" phases - and the liquid-gas phase separating nuclear matter. Major differences between the phase diagrams of the QMD models can be explained by the energy of pure neutron matter at low densities and the saturation density of asymmetric nuclear matter. We show the density dependence of the symmetry energy is also useful to understand uncertainties of the phase diagram. We point out that, for typical nuclear models, the mass fraction of the pasta phases in the later stage of the collapsing cores is higher than 10-20 %.

nucl-th↗

arXiv2009

Formation of Nuclear "Pasta" in Supernovae

In supernova cores, nuclear "pasta" phases such as triangular lattice of rod-like nuclei and layered structure of slab-like nuclei are considered to exist. However, it is still unclear whether or not they are actually formed in collapsing supernova cores. Using {\it ab-initio} numerical simulations called the Quantum Molecular Dynamics (QMD), we here solve this problem by demonstrating that a lattice of rod-like nuclei is formed from a bcc lattice by compression. We also find that, in the transition process, the system undergoes zigzag configuration of elongated nuclei, which are formed by a fusion of two original spherical nuclei.

nucl-th↗

arXiv2007

Impact of nuclear "pasta" on neutrino transport in collapsing stellar cores

Nuclear ``pasta'', nonspherical nuclei in dense matter, is predicted to occur in collapsing supernova cores. We show how pasta phases affect the neutrino transport cross section via weak neutral current using several nuclear models. This is the first calculation of the neutrino opacity of the phases with rod-like and slab-like nuclei taking account of finite temperature effects, which are well described by the quantum molecular dynamics. We also show that pasta phases can occupy 10--20% of the mass of supernova cores in the later stage of the collapse.

astro-ph↗

arXiv2005

Simulation of Transitions between "Pasta" Phases in Dense Matter

Calculations of equilibrium properties of dense matter predict that at subnuclear densities nuclei can be rodlike or slablike. To investigate whether transitions between phases with non-spherical nuclei can occur during the collapse of a star, we perform quantum molecular dynamic simulations of the compression of dense matter. We have succeeded in simulating the transitions between rodlike and slablike nuclei and between slablike nuclei and cylindrical bubbles. Our results strongly suggest that non-spherical nuclei can be formed in the inner cores of collapsing stars.

nucl-th↗

arXiv2003

Nuclear pasta structure in hot neutron stars

Structure of cold and hot dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. Obtained phase diagrams show that the density of the phase boundaries between the different nuclear structures decreases with increasing temperature due to the thermal expansion of nuclear matter region.

astro-ph↗

arXiv2003

Structure of cold nuclear matter at subnuclear densities by Quantum Molecular Dynamics

Structure of cold nuclear matter at subnuclear densities for the proton fraction $x=0.5$, 0.3 and 0.1 is investigated by quantum molecular dynamics (QMD) simulations. We demonstrate that the phases with slablike and rodlike nuclei, etc. can be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape, and also systematically analyze the structure of cold matter using two-point correlation functions and Minkowski functionals. In our simulations, we also observe intermediate phases, which has complicated nuclear shapes. It is found out that these phases can be characterized as those with negative Euler characteristic. Our result implies the existence of these kinds of phases in addition to the simple ``pasta'' phases in neutron star crusts and supernova inner cores. In addition, we investigate the properties of the effective QMD interaction used in the present work to examine the validity of our results. The resultant energy per nucleon $ε_{n}$ of the pure neutron matter, the proton chemical $μ_{p}^{(0)}$ in pure neutron matter and the nuclear surface tension $E_{\rm surf}$ are generally reasonable in comparison with other nuclear interactions.

nucl-th↗

arXiv2002

Microscopic Study of Slablike and Rodlike Nuclei: Quantum Molecular Dynamics Approach

Structure of cold dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We succeeded in showing that the phases with slab-like and rod-like nuclei etc. can be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape. We also observe intermediate phases, which has complicated nuclear shapes. Geometrical structures of matter are analyzed with Minkowski functionals, and it is found out that intermediate phases can be characterized as ones with negative Euler characteristic. Our result suggests the existence of these kinds of phases in addition to the simple ``pasta'' phases in neutron star crusts.

nucl-th↗

arXiv2001

Microscopic Study of Nuclear "Pasta" by Quantum Molecular Dynamics

Structure of cold dense stellar matter at subnuclear densities is investigated with quantum molecular dynamics (QMD). We succeeded in showing that the phases with slab-like and rod-like nuclei etc. can be formed dynamically without any assumptions on the nuclear shape. Our result suggests the existence of these kinds of phases in neutron star crusts.

nucl-th↗