arXiv subjects

Hiroshi Takano

Publications and source records attributed to Hiroshi Takano.

10 recordsLinked to original sources

arXiv2015

Relaxation Mode Analysis and Markov State Relaxation Mode Analysis for Chignolin in Aqueous Solution near a Transition Temperature

It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal component analysis, which extracts modes of large conformational fluctuations around an average structure. We recently applied relaxation mode analysis for protein systems, which approximately estimates the slow relaxation modes and times from a simulation and enables investigations of the dynamic properties underlying the structural fluctuations of proteins. In this study, we apply this relaxation mode analysis to extract reaction coordinates for a system in which there are large conformational changes such as those commonly observed in protein folding/unfolding. We performed a 750-ns simulation of chignolin protein near its folding transition temperature, and observed many transitions between the most stable, misfolded, intermediate, and unfolded states. We then applied principal component analysis and relaxation mode analysis to the system. In the relaxation mode analysis, we could automatically extract good reaction coordinates. The free-energy surfaces provide a clearer understanding of the transitions not only between local minimum-energy states but also between the folded and unfolded states, even though the simulation involved large conformational changes. Moreover, we propose a new analysis method called Markov state relaxation mode analysis. We applied the new method to states with slow relaxation, which are defined by the free-energy surface obtained in the relaxation mode analysis. Finally, the relaxation times of the states obtained with a simple Markov state model and the proposed Markov state relaxation mode analysis are compared and discussed.

physics.chem-ph↗

arXiv2014

Multicomponent Dark Matter in Radiative Seesaw Model and Monochromatic Neutrino Flux

We consider a two loop radiative seesaw model with an exact $Z_2 \times Z'_2$ symmetry, which can stabilize two or three dark matter particles. The model is a simple extension of the inert scalar model of Ma, where the lepton-number violating mass term of the inert scalar, which is required to be small for small neutrino masses, is generated at the one-loop level. The semi-annihilation processes of different dark matter particles, which are present when there exist more than three different dark matter particles, not only play an important role for their relic densities, but also are responsible for the monochromatic neutrino lines resulting from the dark matter annihilation processes. The monochromatic neutrinos do not suffer from a chiral suppression, and we investigate the observational possibility of the monochromatic neutrino flux from the Sun.

hep-ph↗

arXiv2013

Two-loop radiative seesaw with multicomponent dark matter explaining the possible gamma excess in the Higgs boson decay and at the Fermi LAT

A non-supersymmetric model of a two-loop radiative seesaw is proposed. The model contains, in addition to the standard model (SM) Higgs boson, an inert SU(2)_L doublet scalar eta and two inert singlet scalars phi and chi. The lepton number is softly broken by a dimension-two operator, and the tree-level Dirac mass is forbidden by Z_2 x Z_2' (or D_{2N}), which predicts the existence of two or three dark matter particles. The scalar sector is minimal; none of the scalar fields can be suppressed for the radiative seesaw mechanism to work. There are by-products: The SM Higgs boson decay into two gamma's is slightly enhanced by eta^+ (the charged component of eta) circulating in one-loop diagrams for h to gamma gamma. The 135 GeV gamma-ray line observed at the Fermi LAT can be also explained by the annihilation of chi dark matter. We employ a mechanism of temperature-dependent annihilation cross section to suppress the continuum gamma rays and the production of antiprotons. The explanation can survive even down to the XENON1T sensitivity limit.

hep-ph↗

arXiv2012

Multi-Component Dark Matter Systems and Their Observation Prospects

Conversions and semi-annihilations of dark matter (DM) particles in addition to the standard DM annihilations are considered in a three-component DM system. We find that the relic abundance of DM can be very sensitive to these non-standard DM annihilation processes, which has been recently found for two-component DM systems. To consider a concrete model of a three-component DM system, we extend the radiative seesaw model of Ma by adding a Majorana fermion χand a real scalar boson ϕ, to obtain a Z_2 \times Z'_2 DM stabilizing symmetry, where we assume that the DM particles are the inert Higgs boson, χand ϕ. It is shown how the allowed parameter space, obtained previously in the absence of χand ϕ, changes. The semi-annihilation process in this model produces monochromatic neutrinos. The observation rate of these monochromatic neutrinos from the Sun at IceCube is estimated. Observations of high energy monochromatic neutrinos from the Sun may indicate a multi-component DM system.

hep-ph↗

arXiv2012

Spin reversal of a rattleback with viscous friction

Effective equation of motion of a rattleback is obtained from the basic equation of motion with viscous friction depending on slip velocity. This effective equation of motion is used to estimate the number of spin reversals and the rattleback shape that causes the maximum number of spin reversals. These estimates are compared with numerical simulations based on the basic equation of motion.

physics.class-ph↗

arXiv2011

Impact of Inert Higgsino Dark Matter

We consider a recently proposed supersymmetric radiative seesaw model which is coupled with the minimal supergravity. The conventional R parity and $Z_2$ invariance are imposed, which ensures the existence of a multi-component dark matter system. We assume that the pair of the lightest neutralino $\tildeχ$ and the fermionic component $\tildeξ$ of the inert Higgs supermultiplet is dark matter. If $\tildeξ$ is lighter than $\tildeχ$, and the lightest neutral inert Higgs boson is kinematically forbidden to decay (third dark matter), the allowed region in the $m_0{\rm \mathchar`-}M_{1/2}$ plane increases considerably, where $m_0$ and $M_{1/2}$ are the universal soft-supersymmetry-breaking scalar and gaugino mass, respectively, although the dominant component of the multi-component dark matter system is $\tildeχ$. There is a wide allowed region above the recent LHC limit.

hep-ph↗

arXiv2008

Average Structures of a Single Knotted Ring Polymer

Two types of average structures of a single knotted ring polymer are studied by Brownian dynamics simulations. For a ring polymer with N segments, its structure is represented by a 3N -dimensional conformation vector consisting of the Cartesian coordinates of the segment positions relative to the center of mass of the ring polymer. The average structure is given by the average conformation vector, which is self-consistently defined as the average of the conformation vectors obtained from a simulation each of which is rotated to minimize its distance from the average conformation vector. From each conformation vector sampled in a simulation, 2N conformation vectors are generated by changing the numbering of the segments. Among the 2N conformation vectors, the one closest to the average conformation vector is used for one type of the average structure. The other type of the averages structure uses all the conformation vectors generated from those sampled in a simulation. In thecase of the former average structure, the knotted part of the average structure is delocalized for small N and becomes localized as N is increased. In the case of the latter average structure, the average structure changes from a double loop structure for small N to a single loop structure for large N, which indicates the localization-delocalization transition of the knotted part.

cond-mat.soft↗

arXiv2008

Relaxation of a Single Knotted Ring Polymer

The relaxation of a single knotted ring polymer is studied by Brownian dynamics simulations. The relaxation rate lambda_q for the wave number q is estimated by the least square fit of the equilibrium time-displaced correlation function to a double exponential decay at long times. The relaxation rate distribution of a single ring polymer with the trefoil knot appears to behave as lambda_q=A(1/N^)x for q=1 and lambda_q=A'(q/N)^x' for q=2 and 3, where x=2.61, x'=2.02 and A>A'. The wave number q of the slowest relaxation rate for each N is given by q=2 for small values of N, while it is given by q=1 for large values of N. This crossover corresponds to the change of the structure of the ring polymer caused by the localization of the knotted part to a part of the ring polymer.

cond-mat.soft↗

arXiv2003

Self-Diffusion of a Polymer Chain in a Melt

Self-diffusion of a polymer chain in a melt is studied by Monte Carlo simulations of the bond fluctuation model, where only the excluded volume interaction is taken into account. Polymer chains, each of which consists of $N$ segments, are located on an $L \times L \times L$ simple cubic lattice under periodic boundary conditions, where each segment occupies $2 \times 2 \times 2$ unit cells. The results for $N=32, 48, 64, 96, 128, 192, 256, 384$ and 512 at the volume fraction $ϕ\simeq 0.5$ are reported, where $L = 128$ for $N \leq 256$ and L=192 for $N \geq 384$. The $N$-dependence of the self-diffusion constant $D$ is examined. Here, $D$ is estimated from the mean square displacements of the center of mass of a single polymer chain at the times larger than the longest relaxation time. From the data for $N = 256$, 384 and 512, the apparent exponent $x_{\rm d}$, which describes the apparent power law dependence of $D$ on $N$ as $D \propto N^{- x_{\rm d}}$, is estimated as $x_{\rm d} \simeq 2.4$. The ratio $D τ/ < R_{\rm e}^{2} >$ seems to be a constant for $N = 192, 256, 384$ and 512, where $τ$ and $ $ denote the longest relaxation time and the mean square end-to-end distance, respectively.

cond-mat.soft↗

arXiv1996

Instability of the Non-Fermi-Liquid Fixed Point in the Dissipative Gauge Theory of Fermions (I)Impurity Effects

We study a dissipative gauge theory of nonrelativistic fermions in 2+1 dimensions at zero temperature by the Wilsonian renormalization-group method. In this theory, we incorporate in the fermion propagator a new term of the form $ i κ\cdot\sign(ω)$ (where $κ$ is a parameter and $ω$ is the fermion frequency), which is usually induced by impurity effects. In the previous papers, we studied this system for $κ= 0$, and showed that there exists a non-Fermi-liquid infrared fixed point. In this paper, we address the question whether this non-Fermi-liquid behavior remains stable or not in the presence of impurity effects, i.e., the $κ$ term. Our results show that the non-Fermi-liquid fixed point is unstable for $κ\neq 0$ and an effective gauge coupling constant tends to vanish at low energies. However, in intermediate energy scales, the behavior of correlation functions for $κ\neq 0$ is controlled by the non-Fermi-liquid fixed point at $κ=0$, i.e., a crossover phenomenon appears. Physical implications of this phenomenon are discussed.

cond-mat.str-el↗