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Osamu Narikiyo

Publications and source records attributed to Osamu Narikiyo.

31 records · Page 2Linked to original sources
arXiv2011

Codon Capture and Ambiguous Intermediate Scenarios of Genetic Code Evolution

Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our description, a physical quantity, codon level is introduced. In terms of the codon levels two scenarios are typically classified into two different routes of the evolutional process. In the case of the ambiguous intermediate scenario we perform an evolutional simulation implemented cost selection of amino acids and confirm a rapid transition of the code change. Such rapidness reduces uncomfortableness of the non-unique translation of the code at intermediate state that is the weakness of the scenario. In the case of the codon capture scenario the survival against mutations under the mutational pressure minimizing GC content in genomes is simulated and it is demonstrated that cells which experience only neutral mutations survive.

q-bio.GN↗
arXiv2011

Ward identities for anisotropic Cooper pairs

Ward identities for anisotropic Cooper pairs are derived. These for nonlocal pairs have the same form as those for local pairs by employing the pair propagator with the form factor.

cond-mat.supr-con↗
arXiv2009

Scale-free dynamics of somatic adaptability in immune system

The long-time dynamics of somatic adaptability in immune system is simulated by a simple physical model. The immune system described by the model exhibits a scale free behavior as is observed in living systems. The balance between the positive and negative feedbacks of the model leads to a robust immune system where the positive one corresponds to the formation of memory cells and the negative one to immunosuppression. Also the immunosenescence of the system is discussed based on the time-dependence of the epigenetic landscape of the adaptive immune cells in the shape space.

physics.bio-ph↗
arXiv2009

Physical Model for the Evolution of the Genetic Code

We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our model, a minimal model, by introducing a physical quantity, codon level. On the basis of the hierarchical structure of the codon levels two scenarios are classified into two different routes of the evolutional process. In the case of the ambiguous intermediate scenario we perform a simulation implemented cost selection of amino acids and confirm a rapid transition of the code change. Such rapidness reduces uncomfortableness of the non-unique translation of the code at intermediate state that is the weakness of the scenario.

q-bio.PE↗
arXiv2004

Vibration of the Dimer on Ge(001) Surface Excited Coherently by STM Current

The vibration of the dimer on Ge(001) surface with the higher vibrational number excited coherently by STM current is theoretically investigated. The coherent excitation rate of the dimer vibration is obtained by the Hamiltonian consisting of the terms of the electron system and the electron-vibration coupling terms. The transformation of the local structures reported in STM experiments is shown to be driven by the dimer vibration excited coherently by the STM current. The sample bias voltage of STM above which the transtormation to the p(2$\times$2) structure is able to be observed in the experiments, is semiquantitatively reproduced by the quasi-one-dimensional character of the $π^*$-band. We show that the excitation rate has the term not decaying on the distance from the STM tip for the one-dimensional band. The contrastive diffrence of the shapes of the transformed region depending on the sign of the bias voltage observed by the experiments is explained by the difference between the quasi-one-dimensional character of the $π^*$-band and the two-dimensional character of the $π$-band on Ge(001) surface.

cond-mat.mtrl-sci↗
arXiv2003

Vibration of the Dimer on Si(001) Surface Excited by STM Current

The vibration of the dimer excited by STM current on Si(001) surface is investigated. We describe this system by the Hamiltonian which has the electron-vibration coupling term as the key ingredient. In order to characterize the transition rates induced by STM current between vibrational states we have introduced the effective temperature of the vibration which differs from the temperature of the substrate. The behavior of the effective temperature depends on the substrate temperature and STM current in highly nonlinear manner and qualitatively changes around 50K of the substrate temperature. At lower temperatures, the effective temperature strongly deviates from the substrate temperature and reaches a few hundred Kelvin for the typical values of STM current. At higher substrate temperatures, the effective temperature reduces to the substrate temperature. On the basis of these behaviors of the effective temperature, we solve the puzzle of the symmetric-asymmetric crossover in dimer images of STM observation in the ordered state of c(4 x 2).

cond-mat↗
arXiv2001

Enhanced Impurity Scattering due to Quantum Critical Fluctuations

It is shown on the basis of the lowest order perturbation expansion with respect to critical fluctuations that the critical fluctuations give rise to an enhancement of the potential scattering of non-magnetic impurities. This qualitatively accounts for the enhancement of the resistivity due to impurities which has been observed in variety of systems near the quantum critical point, while the higher order processes happen to give much larger enhancement as seen from the Ward identity arguments. The cases with dynamical critical exponent $z$=2 and $z$=3 are discussed explicitly.

cond-mat.str-el↗
arXiv1997

Renormalized Perturbation Approach for Examination of Itinerant-Localized Duality Model for Strongly Correlated Electron Systems

We present a microscopic examination for the itinerant-localized duality model which has been proposed to understand anomalous properties of strongly correlated systems like the heavy fermions by Kuramoto and Miyake, and also useful to describe the anomalous properties of the high-Tc cupurates. We show that the thermodynamic potential of the strongly interacting Hubbard model can be rearranged in the form of duality model on the basis of renormalized perturbation expansion of the Luttinger-Ward functional if the one-particle spectral weight exhibits triple peak structure. We also examine the incoherent degrees of freedom described as a ``localized spin'' and show on the basis of the pertubation expansion that there exists commensurate superexchange-type interaction among the ``localized spins''.

cond-mat.str-el↗
arXiv1994

Aspect of Spin-Charge Separation due to Antiferromagentic Spin Fluctuations in Technically Nested 2D Metals

It is shown that the charge susceptibility in nearly half-filled two-dimensional (2D) metals, with technically nested Fermi surface, shows anomaly at the wavevector different from that for the spin susceptibility at low temperatures. Namely charge degrees of freedom behave there as if their ``Fermi surface" corresponded to that of ``holes" created in the Mott insulator. Such anomaly is caused by the Aslamazov-Larkin type contribution of 2D antiferromagnetic spin fluctuations. This phenomenon gives a possible clue to resolve the paradox of normal state properties of high-$T_{\rm c}$ cuprates {\it starting}\/ from the Fermi-liquid fixed point.

cond-mat↗
arXiv1994

Comment on `Anomalously Large Gap Anisotropy in the a-b Plane of Bi$_2$Sr$_2$CaCu$_2$O$_{8+δ}$'

Comment on `Anomalously Large Gap Anisotropy in the a-b Plane of Bi$_{\bf 2}$Sr$_{\bf 2}$CaCu$_{\bf 2}$O$_{{\bf 8+}δ}$', Kazumasa Miyake and Osamu Narikiyo, In a recent Letter, Shen and collaborators [Phys. Rev. Lett. {\bf 70}, 1555 (1993)] reported that angle-resolved photoemission spectra (ARPES) in Bi-2212 cuprate superconductor far below $T_{\rm c}$ has anomalously large anisotropy and then concluded that the symmetry of Cooper pair is likely to be $d_{x^{2}-y^{2}}$, i.e., $Δ_{\bf k}=Δ(\cos k_{x}a-\cos k_{y}a)$. In this Comment we point out that the interpretation done by Shen {\it et al\/.}, where the shift of edge near Fermi level has been identified with the gap $Δ_{\bf k}$, is not unambiguous, and that a possibility of $d_{xy}$ pairing, i.e., $Δ_{\bf k}=2Δ\sin k_{x}a\sin k_{y}a$, cannot be ruled out.

cond-mat↗
arXiv1993

Excitation Spectrum of a Double Quantum Well System

The collective charge-excitation spectrum of a double quantum well system in a strong magnetic field is obtained within the random phase approximation. Correction to the spectrum coming from the finiteness of the magnetic field is calculated up to the first order in inverse of the magnetic field. Dependencies on the magnetic field of (i) the velocity of long wave length excitation and (ii) the phase boundary of the quantum Hall state signaled by the softening of the roton minimum of the spectrum are discussed. Keywords: quantum Hall effect, two dimensional electrons, strong magnetic field, double quantum well, excitonic state

cond-mat↗