Revising the 4 symmetry in CeCuGe; Soft X-ray absorption and hard X-ray photoemission spectroscopy

荒谷 秀和*; 中谷 泰博*; 藤原 秀紀*; 川田 萌樹*; 金井 惟奈*; 山神 光平*; 藤岡 修平*; 濱本 諭*; 久我 健太郎*; 木須 孝幸*; et al.

Physical Review B, 98(12), p.121113_1 - 121113_6, 2018/09

AA2018-0352.pdf:1.16MB

https://doi.org/10.1103/PhysRevB.98.121113

We present a detailed study on the ground state symmetry of the pressure-induced superconductor CeCuGe probed by soft X-ray absorption and hard X-ray photoemission spectroscopy. The revised Ce ground states are determined as with in-plane rotational symmetry. This gives an in-plane magnetic moment consistent with the antiferromagnetic moment as reported in neutron measurements. Since the in-plane symmetry is the same as that for the superconductor CeCuSi, we propose that the charge distribution along the -axis plays an essential role in driving the system into a superconducting phase.

A New method for evaluating the specificity of indirect readout in protein-DNA recognition

山崎 智*; 寺田 透*; 河野 秀俊; 清水 謙多郎*; 皿井 明倫*

Nucleic Acids Research, 40(17), p.e129_1 - e129_7, 2012/09

https://doi.org/10.1093/nar/gks462

Proteins recognize a specific DNA sequence not only through direct contact (direct readout) with base pairs but also through sequence-dependent conformation and/or flexibility of DNA (indirect readout). However, it is difficult to assess the contribution of indirect readout to the sequence specificity. What is needed is a straightforward method for quantifying its contributions to specificity. Using Bayesian statistics, we derived the probability of a particular sequence for a given DNA structure from the trajectories of molecular dynamics (MD) simulations of DNAs containing all possible tetramer sequences. Then, we quantified the specificity of indirect readout based on the information entropy associated with the probability. We tested this method with known structures of protein-DNA complexes. This method enabled us to correctly predict those regions where experiments suggested the involvement of indirect readout. The results also indicated new regions where the indirect readout mechanism makes major contributions to the recognition. The present method can be used to estimate the contribution of indirect readout without approximations to the distributions in the conformational ensembles of DNA, and would serve as a powerful tool to study the mechanism of protein-DNA recognition.

Deuterium depth profiling in JT-60U W-shaped divertor tiles by nuclear reaction analysis

林 孝夫; 落合 謙太郎; 正木 圭; 後藤 純孝*; 沓掛 忠三; 新井 貴; 西谷 健夫; 宮 直之

Journal of Nuclear Materials, 349(1-2), p.6 - 16, 2006/02

https://doi.org/10.1016/j.jnucmat.2005.06.019

核反応分析法(NRA)を用いてJT-60Uダイバータ部のプラズマ対向壁に用いられている炭素タイル中の重水素保持量深さ分布を測定した。最も重水素濃度が高かったのは外側ドームウィングタイルでD/Cの値は0.053であり、その重水素蓄積過程は炭素-重水素の共堆積によるものと推定された。また外側及び内側のダイバータターゲットタイルにおいてはD/Cは0.006以下であった。軽水素を含めた水素同位体の濃度については、NRA及びSIMS分析結果からドーム頂部タイルの(H+D)/Cを0.023と推定した。一方OFMC計算を用いてNBIで入射した高エネルギー重水素がドーム領域に打ち込まれることを示した。また重水素の打ち込みや炭素との共堆積などによる重水素蓄積は、タイルの表面温度や損耗・堆積などの表面状態の影響を受けることを示した。重水素保持量深さ分布,SEM分析及びOFMC計算により、重水素分布はおもに重水素-炭素の共堆積,重水素イオンの打ち込み及びバルクへの拡散の複合したプロセスにより決まることを明らかにした。

Measurement of deuterium and tritium retentions on the surface of JT-60 divertor tiles by means of nuclear reaction analysis

落合 謙太郎; 林 孝夫; 沓掛 忠三; 後藤 純孝*; 正木 圭; 新井 貴; 宮 直之; 西谷 健夫

Journal of Nuclear Materials, 329-333(Part1), p.836 - 839, 2004/08

https://doi.org/10.1016/j.jnucmat.2004.04.292

FNSでは重陽子加速器ビームによる核反応分析法を用いて、黒鉛実機ダイバータ表面のDとTの保持量及び深さ分布について測定を行った。測定対象である黒鉛ダイバータは2つである。利用核反応と検出荷電粒子はD分布測定の場合、D(d,p)T核反応によるプロトン粒子を、T分布測定の場合はT(d,)n核反応による粒子である。D(d,p)T核反応によるプロトンとトリトン及びC(d,p)Cのプロトンのスペクトルピークが得られており、その検出エネルギーは計算で求まる試料表面からの放出エネルギーとよく一致していることから、重水素が試料表面からmオーダーで深く堆積していることが明らかとなった。これらの収量から重水素の平均保持量は内側ダイバータで約110cmであり、トリチウムベータ線の放射能は18kBq/cmに相当するという結果を得た。また350keV入射のみアルファスペクトルを得ている結果から、トリチウムの深さ分布については母材2mより深い位置にあると考えられる。

Neutron transmission experiment of boron-doped resin for the JT-60SC neutron shield using 2.45 MeV neutron source

森岡 篤彦; 佐藤 聡; 落合 謙太郎; 逆井 章; 堀 順一; 山内 通則*; 西谷 健夫; 神永 敦嗣; 正木 圭; 櫻井 真治; et al.

Journal of Nuclear Science and Technology, 41(Suppl.4), p.109 - 112, 2004/03

http://www.tandfonline.com/doi/abs/10.1080/00223131.2004.10875657

定常炉心試験装置(JT-60SC)のポート部分の中性子遮へいは、ポリエチレンよりも温度特性に優れたレジン(商標名: KRAFTON)を使用した設計となっている。超伝導コイルの核発熱量低減のための遮へい性能を保ちつつ、ポート重量を軽減させるため、筆者らはレジンに天然ボロンを添加した、ボロン入りレジンを開発した。ボロン添加量を変えた数種類の試料に、DD反応で発生する2.45MeV中性子を照射し、透過中性子を測定し、ボロン入りレジンの遮へい性能を比較した。高速中性子の遮へい性能はボロン添加量に依存せず同じであった。一方、低エネルギー中性子の遮へい性能はボロン2重量%の試験体がボロン1重量%の試験体より約25%良く、ボロン添加の効果が観測された。

Role of indirect readout in protein-DNA recognition assessed by a Bayesian approach

山崎 智*; 福井 一彦*; 河野 秀俊; 清水 謙多郎*; 皿井 明倫*; 寺田 透*

no journal, , 

Sequence-specific recognition of DNA by proteins plays a critical role in regulating gene expression. Accurate recognition is achieved by a combination of two different mechanisms. The first is direct readout, in which recognition is mediated by direct interactions between the protein and the DNA bases. The second is indirect readout, which is caused by the sequence-dependence of the conformation and deformability of the DNA structure. In our previous study, the contributions of indirect readout to binding affinity were evaluated for every tetrameric step in given protein-DNA complex structures. Using sequence-structure threading, potential energy differences between native and non-native tetrameric sequences for given tetrameric step conformation were compared. These potential energy functions were derived from the probability distribution function of its tetrameric step conformations calculated from trajectories of MD simulations of free DNAs which include all 136 types of tetramers. This gave good agreement with some experimental results, but shortage of structural sampling made the accurate estimation of distribution function difficult. In this work, we estimate the probability of occurrence of each tetrameric step sequence on given tetrameric step conformation using a Bayesian approach using the same structural dataset. We apply this approach to known protein-DNA complex structures, and assess the performance of predicting the sequence region where indirect readout makes important contribution to the binding affinity.

A New method for evaluating the specificity of indirect readout in protein-DNA recognition

山崎 智*; 寺田 透*; 河野 秀俊; 清水 謙多郎*; 皿井 明倫*

no journal, , 

Sequence-specific recognition of DNA by proteins plays a critical role in regulating gene expression. The accurate recognition of target sequences in the genome can be achieved by a combination of two different mechanisms: the direct readout through the direct interactions between protein and DNA bases; and the indirect readout through the sequence-dependent conformation and/or deformability of DNA structure. While the specificity of direct readout has been well characterized, it is rather difficult to assess the contribution of indirect readout to the specificity. In order to quantify the specificity of indirect readout, we have developed a new method. First, we used Bayesian statistics to derive the probability of a particular sequence for a given DNA structure using ensembles obtained by molecular dynamics (MD) simulations of DNAs containing all 136 unique tetramer sequences. Secondly, we used the information entropy to quantify the specificity of indirect readout. We applied this method to protein-DNA complexes of known structures to examine its validity. We could correctly predict those regions where experiments suggested the involvement of indirect readout, and could indicate new regions where the indirect readout mechanism can make major contributions to the recognition. The present probability/entropy-based approach has advantage over the previous energy-based approach in that the trajectories of MD simulation can be directly converted into the probability of sequence and the specificity of indirect readout without any approximation to the distributions in the conformational ensembles of DNA, and would serve as a powerful tool to study the mechanism of protein-DNA recognition.