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Yoji Nakamura

Publications and source records attributed to Yoji Nakamura.

4 recordsLinked to original sources
arXiv2022

Disentanglement of intrinsic and extrinsic side-jump scattering induced spin Hall effect in N-implanted Pt

The rapidly evolving utilization of spin Hall effect (SHE) arising from spin-orbit coupling in 5d transition metals and alloys have made giant strides in the development of designing low-power, robust and non-volatile magnetic memory. Recent studies, on incorporating non-metallic lighter elements such as oxygen, nitrogen and sulfur into 5d transition metals, have shown an enhancement in damping-like torque efficiency θ_DL due to the modified SHE, but the mechanism behind this enhancement is not clear. In this paper, we study θ_DL at different temperatures (100-293 K) to disentangle the intrinsic and extrinsic side-jump scattering induced spin Hall effect in N-implanted Pt. We observe a crossover of intrinsic to extrinsic side-jump mechanism as the implantation dose increases from 2*10^16 ions/cm2 to 1*10^17 ions/cm2. A sudden decrease in the intrinsic spin Hall conductivity is counterbalanced by the increase in the side-jump induced SHE efficiency. These results conclude that studying θ_DL as a function of implantation dose, and also as a function of temperature, is important to understand the physical mechanism contributing to SHE, which has so far been unexplored in incorporating non-metallic element in 5d transition metals.

cond-mat.mtrl-sci↗
arXiv2017

A mathematical model for gene evolution after whole genome duplication

Whole genome duplication (WGD) is one of the most important events in the molecular evolution of organisms. In fish species, a WGD is considered to have occurred in the ancestral lineage of teleosts. Recent comprehensive ortholog comparisons among teleost genomes have provided useful data and insights into the fate of redundant genes generated by WGD. Based on these data, a mathematical model is proposed to explain the evolutionary scenario of genes after WGD. The model is parameterized taking into account an equilibrium between i) rapid loss of either of the duplicate genes and ii) moderate functional differentiation of each of duplicate genes, both of which are followed by slow gene loss under purifying selection. This model predicts that, in the teleost lineage, a maximum of about 3000 gene pairs may have differentiated functionally during 90 million years after WGD. Thus, the present study provides a possibility that the whole impact of WGD can be quantitatively assessed according to the model parameters, before details of genomic structural changes or functional differentiation are investigated. If the equilibrium model is valid not only for teleosts but also for other lineages that have undergone WGDs, correlations between the assessment indices and evolutionarily significant events, such as the diversification of species or the occurrence of novel phenotypes, could be tested and compared among those lineages.

q-bio.PE↗
arXiv2006

Gene cluster analysis method reliably identifies horizontally transferred genes and reveals their involvement in operon formation

The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur, definitive concrete cases have been unavailable. It is desirable to select horizontally transferred genes reliably and examine their relationship to operons. We here developed a method to identify candidates of horizontally transferred genes based on minimization of gene cluster insertions/deletions. To select a benchmark set of positively horizontally transferred genes against which the candidate set can be appraised, we devised another procedure using intergenetic alignments. Comparison with the benchmark set of horizontally transferred genes demonstrated the absence of a significant number of false positives in the candidates, showing that the method identifies horizontally transferred genes with a high degree of confidence. Horizontally transferred genes constitute at least 5.5% of the genes in Escherichia, Shigella, and Salmonella and ~46% of which originate from other gamma-proteobacteria. Not only informational genes, but also operational genes (those involved in housekeeping) are horizontally transferred less frequently than expected. A gene-cluster analysis of Escherichia coli K-12 operons revealed that horizontal transfer produced four entire operons and expanded two operons, but deletion of intervening genes accounts for the formation of no operons. We propose that operons generally form by horizontal gene transfer. We further suggest that genes with related essential functions tend to reside in conserved operons, while genes in nonconserved operons generally confer slight advantage to the organisms and frequently undergo horizontal transfer and decay.

q-bio.PE↗