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| 1.
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KURNIAWAN, Isman ; Kawaguchi, Kazutomo ; SUGIMORI, Kimikazu ; SAKURAI, Takeshi ; Nagao, Hidemi
概要:
We present a cluster model representing type I copper (T1Cu) center of copperprotein, which corrsponds to Multicopper Oxidases, Azurin, Stelacyanin and so on. Theelectronic structure and physical properties such as molecular
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orbital, atomic partial charge,partial spin densities, ionization energy (IP) of reduced T1Cu, electron affinity (EA) of oxidizedT1Cu, the bond and the angle constants etc. are calculated by using two typicalDensity Functional Theory (DFT) functionals, which are B3LYP and M06, with 6-31G(d)basis set. We find the dependency of several properties such as atomic partial charge, partialspin densities, IP, and EA on the DFT functionals. We also find that the DFT functionals givea better contribution to bond constants, especially in case of the interaction between copperand the axial ligand. We calculate the maximum absorption wavelength of T1Cu center andfind relatively a good agreement with experimental data.
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| 2.
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ARWANSYAH, MS ; KODAMA, Koichi ; KURNIAWAN, Isman ; KATAOKA, Tatsuki ; Kawaguchi, Kazutomo ; Nagao, Hidemi
概要:
We investigate the binding/dissociation process of ligand molecule from carbonicanhydrase (CA) I carbonic anhydrase (CA) I enzyme by using all-atom moleculardynamics simulation. The force field parameters of zinc ion in the CA I
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active site are estimatedby quantum chemical calculations and are summarized in this paper. The free energyprofile for binding/dissociation process of ligand from CA I active site is calculated by thethermodynamic integration combined with the all-atom molecular dynamics simulation. Thebinding free energy as a function of the distance between the center of mass positions of CAI active site and the ligand molecule is estimated. The radial distribution function of theCA I-ligand complex is calculated from the trajectory of all-atom molecular dynamics (MD)simulation. We estimate the free energy surface from the radial distribution function. Wecan obtain the bond constant of the equilibrium state from the value of the free energy surface.We discuss the binding/dissociation process of ligand molecule by calculating the freeenergy profile to know the stability of the CA I-ligand complex with some thermodynamicproperties such as the binding free energy, the equilibrium state of the free energy surfaceand so on.
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| 3.
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Sugimori, Kimikazu ; Shuku, Tomofumi ; Sugiyama, Ayumu ; Nagao, Hidemi ; Sakurai, Takeshi ; Nishikawa, Kiyoshi
概要:
We present a cluster model for the active site of oxidized azurin, and investigate the electronic structure of the activ
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e site of oxidized azurin by using density functional calculations with polarizable continuum model. The singly occupied molecular orbital and spin density in the model widely distribute around the Cu 3dx2-y2 and S(Cys112) 3p orbitals. The dependency of electronic properties such as partial charge density and spin density on the dielectric constant is discussed. We find that partial spin density and charge density on the copper ion become larger, when the dielectric constant increases. © 2005 Elsevier Ltd. All rights reserved.<br />Embargo Period 24 months
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| 4.
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Oda, Tatsuki ; Sugimori, K. ; Nagao, Hidemi ; Hamada, I. ; Kagayama, S. ; Geshi, M. ; Nagara, H. ; Kusakabe, K. ; Suzuki, N.
概要:
金沢大学大学院自然科学研究科計算科学<br />金沢大学工学部<br />We have studied the ζ-phase of solid oxygen using the generalized gradient approxim
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ation in the density functional approach. Calculations of total energies and pressures have been carried out for the prototype of diatomic ζ-phase and other hypothetical monoatomic crystal structures. The diatomic phase was found to be stable over a wide range of pressure (100-2000GPa). The stacking of molecular layers is discussed in comparison with the available experimental data. © IOP Publishing Ltd.
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| 5.
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Takamatsu, Yuichiro ; Sugiyama, Ayumu ; Purqon, Acep ; Nagao, Hidemi ; Nishikawa, Kiyoshi
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金沢大学大学院自然科学研究科計算科学<br />金沢大学理学部<br />Recently, much attention has been directed to calculational prediction for binding
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free energy and structural analysis for biomolecule complex in solvate state. We investigated Influenza Hemagglutinin (wild type HA), mutated HA and its neutralize antibody Fab fragment complex in explicit solvent water molecules by molecular dynamics simulation(MD). B-factor and binding free energy of loop structures in the complex structure are calculated. The calculation result supports the experimental result in a qualitative tendency. MD calculation also shows that hydrogen bond distance differs between wild type HA and mutated HA, which contributes to the difference of binding free energy and structural stability. These result suggests that pattern of making hydrogen bonds in crystal structure are almost kept even in solvate state. © 2006 American Institute of Physics.
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| 6.
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Sugiyama, Ayumu ; Takamatsu, Yuichiro ; Purqon, Acep ; Mizukami, Taku ; Nagao, Hidemi ; Nishikawa, Kiyoshi
概要:
金沢大学大学院自然科学研究科計算科学<br />金沢大学理学部<br />We carry out the molecular dynamics(MD) simulation of type 1 blue copper protein az
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urin in room and some lower temperatures to investigate the behavior of hydration water molecules in the protein surface. In this study, we find the anomalous behavior of the water molecules, which depend on the system temperatures. These water molecules have hydrogen bond to the protein surface residues. We specify the residues type, being classified as the hydration donor and the hydration acceptor of water molecules. We analyze the residue type, and the bond length and bond strength between solvent water molecules in each temperature. Moreover, we estimate the B-factor of these residues which indicates the fluctuation of hydration residues in each temperature. B-factor values depend on the system temperatue althought the number of hydration residue do not depend on the temperature. © 2006 American Institute of Physics.
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| 7.
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Purqon, Acep ; Sugiyama, Ayumu ; Takamatsu, Yuichiro ; Nagao, Hidemi ; Nishikawa, Kiyoshi
概要:
金沢大学大学院自然科学研究科計算科学<br />金沢大学理学部<br />Some proteins in blue copper proteins have similar properties. In some cases it is
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not easy to distinguish the proteins each other. The study to recognize and classify in blue copper proteins has important roles to recognize the difference of similar properties, for examples, structures and residue sequences in blue copper proteins. There are many methods being developed to predict protein structure from many approachs, which one still not satisfactory yet. Therefore it is a challenge for scientists to develop or improve their methods. One of promising method is artificial neural networks (ANN). ANN is learning machine methods consisted of input, hidden and output layer. ANN is tested to recognize secondary structure in blue copper protein. It is found that ANN can distinguish for 7-type of secondary structure and recognize 72% secondary structure in blue copper protein. © 2006 American Institute of Physics.
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| 8.
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Oda, Tatsuki ; Sugimori, K. ; Nagao, Hidemi ; Hamada, I. ; Kagayama, S. ; Geshi, M. ; Nagara, H. ; Kusakabe, K. ; Suzuki, N.
概要:
金沢大学理工研究域 数物科学系<br />We have studied the ζ-phase of solid oxygen using the generalized gradient approximation in the den
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sity functional approach. Calculations of total energies and pressures have been carried out for the prototype of diatomic ζ-phase and other hypothetical monoatomic crystal structures. The diatomic phase was found to be stable over a wide range of pressure (100-2000GPa). The stacking of molecular layers is discussed in comparison with the available experimental data. © IOP Publishing Ltd.
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| 9.
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Sri, R. Natasia ; Saito, Hiroaki ; Mizukami, Taku ; Kawaguchi, Kazutomo ; Nagao, Hidemi
概要:
Solvation free energy has valuable role as represents the desolvation cost of a molecu-lar binding interaction, which is
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very important in a variety of chemical and biological processes. Therefore, many computational methods have been explored to predict this value. In this study, we attempted to find the correlation between experimental and calculated value of solvation free energy of proteins, containing organic molecules, by using quantitative structure property relation-ship (QSPR) model. To obtained a comparable value of solvation free energy which will be used as reference in QSPR model, we adopted energy representation (ER) method. And as this method works through molecular dynamic (MD) simulation, we then performed the MD simulation prior to the calculation by ER method. The results showed that the predicted solvation free energies were quite close to calculated values by ER method. We also found that the values of solvation free energy, both in MD simulation and ER method, were well correlated to solvent accessible surface area of hydrophobic portion.<br />Selected Papers from the International Symposium on Computational Science - International Symposium on Computational Science Kanazawa University, Japan
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| 10.
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Iwayama, Masashi ; Kawafuchi, Kazutomo ; Saito, Hiroaki ; Nagao, Hidemi
概要:
We have been applied the conventional approach based on the molecular dynamics simulation to estimate the redox potential so far. In this study, we have focused the computational conditions in order to estimate standard redox
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potential by using the energy representation method: we calculate excess chemical potential increasing the number of solvent molecules and sampling data for the preparation of energy distribution functions. From these results, we have found that the computational value of the standard redox potential is close to the experimental value in the case of the system with larger number of solvent molecules unaffected by the behavior of counter-ion when we take a sufficient sampling data for the energy distribution functions.<br />Selected Papers from the International Symposium on Computational Science - International Symposium on Computational Science Kanazawa University, Japan
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| 11.
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Kurniawan, Isman ; Saito, Hiroaki ; Kawaguchi, Kazutomo ; Nagao, Hidemi
概要:
This study focus on investigating the oxidation potential fluctuation of organic molecule in the solution. The organic mo
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lecule that was investigated is 3-pentanone molecule that has oxi-dation potential 0.143 V experimentally. The oxidation potential was calculated using Born-Haber cycle approximation involving the calculation of gas phase Gibbs free energy and solvation energy of reduced and the oxidized state. The reduced state represents a neutral charge molecule and the oxidized state represents a radical cation molecule. The first, molecular dynamics (MD) simulation of both state was performed for 2 ns time. Then, 400 snapshot structures of both state molecule was captured. Gas phase Gibbs free energy and solvation energy were calculated using MP2 theory with cc-pvdz basis set and the solvation effect was approached using Polarizable Continuum Model (PCM). Normal Hydrogen Electrode (NHE), that has redox potential 4.44 V experimentally, was used as reference electrode. The result shows the different of gas phase Gibbs free energy average of both state was 756.97 ± 21.598 kJ/mol, and solvation energy average of reduced and oxidized state were -18.42 kJ/mol ± 1.482 kJ/mol, and -219.02 ± 1.094 kJ/mol respectively. Then, the oxidation potential was calculated by substituting gas phase Gibbs free energy and solvation energy into Born-Haber cycle approximation. The calculation result shows the average of oxidation po-tential value is 1.396 ± 0.225 V. The deviation of oxidation potential confirms the fluctuation of oxidation potential during the simulation.
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| 12.
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Iwayama, Masashi ; Kawaguchi, Kazutomo ; Saito, Hiroaki ; Nagao, Hidemi
概要:
Structure and hydration property of acetone and 3-pentaone in the neutral and cationic state were investigated by using molecular dynamics (MD) and free energy calculations. The force field parameters of stretching vibration, angle
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bending, and partial charges of each molecule in the neutral and cationic state were developed by using density functional theory (DFT) calculations with B3LYP method and 6-31+G** basis set. The optimized structures by using these force field parameters in gas phase were compared with the experimental data and AMBER force fields parameters (parm99). From the results, the optimized structure in the neutral state of acetone was in good agreement with the experimental data. The evaluated hydration free energy in the neutral state of acetone was closed to the experimental data, while that of 3-pentaone was little bit larger than the experimental data. The ionization effect of ketone molecule on the hydration free energies was found to be significant in both molecules.
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| 13.
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Meidy, Triana Pakpahan ; Saito, Hiroaki ; Kawaguchi, Kazutomo ; Nagao, Hidemi
概要:
Accurate methods of computing the affinity of ligand with protein target are strongly needed in the drug discovery proce
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ss. Many attempts have been made and several algorithms have been developed for this purpose. We compared the protein-ligand binding free energies (∆G) in various methods include docking score function, combining docking score function and molecular dynamics (MD) simulation with explicit and implicit solvent model, and molecular-mechanics Poisson Boltzmann surface area (MM-PBSA) approach with and without the inclusion of entropic contributions. We tested these various methods to human plasminogen kringle-3 domain protein with the ligand trans-(aminomethyl) cyclohexanecarboxylic acid (AMCHA). The results showed the comparison between these various methods and the experimental affinity value. We found that combining docking score function and MD simulation with explicit solvent model was more favorable and close to the experimental result. This indicated that combining docking score function and MD simulation with explicit solvent model could be more accurate and effective in the protein-ligand binding free energy calculation.
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| 14.
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Micke, Rusmerryani ; Takasu, Masako ; Kawaguchi, Kazutomo ; Saito, Hiroaki ; Nagao, Hidemi
概要:
Most of protein function analyses focus mainly on the physical properties of a sin-gle protein. Nevertheless, the enviro
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nments where proteins perform their biological functions are crowded with macromolecules, such as lipid, nucleic acids, and other proteins. The interactions between macromolecules may be affected by molecular crowding. Therefore, as an initial step we here investigate the protein–protein interactions for gaining insights into molecular crowding effects on protein conformational changes. Computational molecular simulation is one of the useful and important tools to study the protein interactions. Here we develop a coarse-grained model and a topology-based potential interactions to simulate dynamical properties of multiprotein complex crys-tal structure. We apply them to simulate complex crystal structure of Pseudomonas Aeruginosa azurin, a small cupredoxin, which functions as an electron carrier in bacterial respiration. Since electron transfer on azurin plays an important role in the biological system, it is important to cha-racterize the protein interactions in azurin. In our simulation, the interactions between intra- and inter- domains are treated at the residue level with the implementation of the off lattice G¯o-like model. In each domain, bonded interactions between residues are described by bond stretching, bond angle bending, and torsional angle potentials. The non-bonded interactions, which are repre-sented by short range and long range potentials, describe the interactions both among residues and between proteins. We probe the protein–protein interactions by analyzing the protein binding. A simple clustering algorithm is applied to group the bound structures of protein complex. Moreover, we can investigate the importance of the long range interaction on the multiprotein complex system. These studies will serve as valuable insights for further investigation on molecular crowding effects.
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| 15.
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Muhamad, Koyimatu ; Shimahara, Hideto ; Kawaguchi, Kazutomo ; Saito, Hirosaki ; Sugimori, Kimikazu ; Nagao, Hidemi
概要:
Human carbonic anhydrase II (HCA II) catalyses the reversible hydration of CO2. In this enzyme, the imidazole ring of hi
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stidine at position 64 (His64) functions to transfer the productive proton from the zinc-bound water to the buffer molecule in bulk-water. X-ray data of HCA II show that His64 has two types of side chain orientations, ”in” and ”out”, representing the direction of the imidazole ring toward and away from the active site, respectively. Maupin et al. reported that the imidazole of His64 can be rotated in a model system of the active site to clarify the proton transfer of catalytic mechanism. However, the indole ring of tryptophan at position 5 (Trp5) that is located near the ”out” of the imidazole ring of His64 was not considered in the model system. In this study, in order to estimate detailed rotational properties of His64, we constructed two His64-containing models with and without Trp5, and then simulate the constructed structures by using MP2 method and 6-311++G(d,p) basis sets. This allows us to tentatively determine the potential energies of the π-stacking interaction of the imidazole with the indole in relation to the side chain rotation of His64. The result indicates that the π-stacking interaction causes an increase of the energy barrier between ”in” and ”out” conformations, implying that the rotational motion of His64 is not relevant to explain the proton transfer during catalysis. Alternatively, a steady position of His64 would be needed in the proton transfer in catalytic mechanism of HCA II.
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| 16.
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Micke, Rusmerryani ; Gia, Septiana ; Kawamoto, Shuhei ; Hiroaki, Saito ; Nishikawa, Kiyoshi ; Nagao, Hidemi
概要:
Due to the soft and flexible structure, lipid molecule forms various shapes such as micelle, bilayer and vesicle. In thes
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e systems, since the spherical micelle can be applied to the application of drag delivery system, the analysis of detailed structure and dynamics of the micelle is important. In this study, we carried out molecular dynamics (MD) simulations of the spherical micelles dimer in water solvent to investigate the dynamical structure and correlated motion of the micelle dimer. The MD simulations were run under the constant NPT and NVT conditions with periodic boundary. We adopted the ASIC analysis, which is based on the aperture, symme-try, isotropy, and compactness of the micelle structure to analyze the shape fluctuations for each micelle. From this analysis, we show the stability and correlated motion of spherical micelle and investigate the patterns of synchronization motions between micelle dimer. The mutual fluctuations were periodically shown in the constant NVT simulation, implying that the existence of synchro-nization phenomena between micelle dimer.
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| 17.
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Septiana Wulandari, Gia ; Rusmerryani, Micke ; Kawamoto, Shuhei ; Saito, Hiroaki ; Nishikawa, Kiyoshi ; Nagao, Hidemi
概要:
We studied the temperature effect on the dynamics of spherical micelle dimer in wa-ter solvent by using molecular dynamic
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s (MD) simulation. For this purpose, we carried out the MD simulations of 8-8 spherical POPC micelle dimer in 11,326 TIP3P water molecules under the constant NPT condition for 10 ns and continued the MD simulation under the constant NVT condition for 10 ns. We ran the MD simulations of this system at two different temperatures, 340 K and 370 K. The dynamical behavior of the micelle was analyzed by calculating ASIC parameters. We found that the effects of temperature on stuctures and dynamics of micelle were different for the constant NPT and NVT condition.
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| 18.
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長尾, 秀実 ; Nagao, Hidemi
概要:
金沢大学理工学域数物科学系<br />X線構造解析により酸化型アズリン(Az)と還元型シトクロムc551(Cyt)の構造が知られている。各立体構造にプロトンを付加し、各活性部位付近の必要パラメータを各活性部位類似のクラスターモデルを用いて密
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度汎関数法(UB3LYP/6-31G^<**>/ESP)により見積もった。これらの立体構造を用いてAz_<ox>-Cyt_<red>複合体構造最適化をZDOCKプログラムパッケージおよび独自開発プログラムで予測した。これらの座標データから3つの複合体モデルを作成した。(1)水素結合を含む静電相互作用エネルギーを最小にしたモデル。(2)疎水性相互作用エネルギー最小にした構造。(3)活性部位の電荷分布をAz_<red>-Cyt_<ox>型にしたモデル。これら3通りのモデルよるタンパク質複合体の溶液内での安定性を溶媒和自由エネルギー計算に評価した。計算した構造エネルギーに溶媒和自由エネルギー,エントロピーを加えることで新しく定義したタンパク質の自由エネルギーの計算結果は活性部位の電荷分布をAz_<red>-Cyt_<ox>型にしたモデルが最も低い値を示した。結合自由エネルギーの評価には、複合体を形成する前のAz_<ox>単体の構造とCyt_<red>単体の構造における溶媒和エネルギー,構造エネルギー,エントロピーを評価し、タンパク質複合体の自由エネルギーとの差から評価した。Az_<ox>, Cyt_<red>単体と複合体の自由エネルギーの差は-107kcal/mol、構造エネルギーの差は-47kcal/mol、エントロピーの差は31kcal/molとなった。これらの結果から結合自由エネルギーの値は-123kcal/molであることが示され、タンパク質複合体の結合自由エネルギーには溶媒和自由エネルギーが大きく寄与していることがこれらの計算結果から示された。<br />研究課題/領域番号:20038018, 研究期間(年度):2008 – 2009
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| 19.
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長尾, 秀実 ; Nagao, Hidemi
概要:
金沢大学自然科学研究科<br />X線構造解析により知られている酸化型アズリン(Az_<ox>)と還元型シトクロム(Cyt_<red>)の立体構造を用いてAz_<ox>-Cyt_<red>複合体構造最適化をZDOCKプログラムパッケージおよ
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び独自開発プログラムで予測した。Amber力場と活性部位付近の量子化学計算で見積もられた力場を用い、5854個のTIP5P水分子を加えた系を300K、NVTアンサンブル条件下でシミュレーションした。シミュレーションによりAz_<ox>-Cyt_<red>複合体安定構造を見いだした。ドッキングサイトは二つの部分に分けられ、いずれの部分もターン構造中にあり、水素結合で強く結合しAz_<ox>-Cyt_<red>複合体を形成していることがわかった。本研究により複合体に関わる水素結合部位が明確に示された。次にAz_<ox>-Cyt_<red>複合体ダイナミックスを考察した。会合前後でCyt_<red>タンパク質振動が大きく変わっていることが見いだせた。またドッキングサイトではAz_<ox>とCyt_<red>との協調的振動モードが現れ、タンパク質構造変化のみならず、振動主成分変化が観測された。還元型アズリン(Az_<red>)は空気中酸素により酸化され結晶化が容易ではない。Az_<red>-Cyt_<ox>複合体構造決定もまた、空気中酸素による複合体酸化が起こるため現在のところ実験で決定するのは容易ではない。そこでAz_<red>-Cyt_<ox>複合体における各活性部位付近の電荷分布を用いた構造緩和シミュレーションを行った。Amber力場と活性部位付近の量子化学計算で見積もられた力場を用い、6204個のTIP5P水分子を加えた系を300K、NVTアンサンブル条件下でシミュレーションした。構造緩和後、複合体安定構造を見いだした。Az_<red>-Cyt_<ox>複合体ドッキングサイトはAz_<ox>-Cyt_<red>複合体のものとほぼ一致していることを見いだした。またDynamical Cross Correlation MapによりAz_<red>のαヘリックスとCyt_<ox>のほぼ全体が強く動的相関を持つことが見いだされた。一般にタンパク質ターン構造部分はB因子(RMSF)が最も大きく、次にαヘリックス部分が大きい。本研究結果からターン構造部分にドッキング部位があり、AzとCytのドッキングによりターン構造部分の運動が束縛される。そしてαヘリックス部分へのエネルギー移動が示唆される。<br />研究課題/領域番号:19029014, 研究期間(年度):2007<br />出典：「タンパク質複合体構造とダイナミックスの理論的研究」研究成果報告書 課題番号19029014（KAKEN：科学研究費助成事業データベース（国立情報学研究所））（https://kaken.nii.ac.jp/ja/grant/KAKENHI-PROJECT-19029014/)を加工して作成
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| 20.
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長尾, 秀実 ; Nagao, Hidemi
概要:
金沢大学理工研究域数物科学系<br />本研究ではスピン状態のレーザー制御シミュレーションおよび二原子分子の多光子吸収過程に関する理論的研究を展開した。(1)スピン状態のレーザー制御シミュレーションCl_2分子とO_2分子のスピン状態一重項
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-三重項遷移の光制御に関する理論的研究を行った。スピン-軌道相互作用を考慮にいれたスピン混合状態のab initio計算を行い、核の運動をあらわに取り込んだ光誘起ポテンシャル断熱通過(APLIP)法を適用した。Cl_2分子では三重項励起状態に一度は遷移するが、中間状態、目的状態ともに解離状態であるため解離することが分かった。O_2分子では最終的な目的状態のポピュレーションは99.5%となり、ほぼ完全に三重項基底状態から一重項励起状態へのスピン状態の制御を実現したが、遷移双極子モーメントの値は非常に小さいため適切な電場強度にするにはパルス幅を広くとる必要が分かった。(2)二原子分子の多光子吸収過程の理論的研究OH分子の電子状態計算によりポテンシャル曲線、遷移双極子モーメントの行列要素を計算しモースポテンシャルパラメータを決定した。基底状態からの1光子から4光子吸収過程までのシミュレーションに成功した。次に多光子吸収過程を利用した状態制御として2光子吸収を用いた誘導ラマン断熱通過法(STIRAP)のシミュレーションに成功した。核の運動をあらわに取り込んだ光誘起ポテンシャル断熱通過(APLIP)法を用いて多光子吸収過程のシミュレーションにより2光子吸収を用いた誘導ラマン断熱通過法(STRAP)による状態制御の可能性が示すことができた。<br />研究課題/領域番号:16032204, 研究期間(年度):2004-2005<br />出典：「レーザー照射による結晶の物性発現と制御に関する理論的研究」研究成果報告書 課題番号16032204（KAKEN：科学研究費助成事業データベース（国立情報学研究所））（https://kaken.nii.ac.jp/ja/grant/KAKENHI-PROJECT-16032204/)を加工して作成
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| 21.
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長尾, 秀実 ; Nagao, Hidemi
概要:
金沢大学理工研究域数物科学系<br />本研究ではレーザー照射による酸化物高温超伝導体における電子移動および酸素原子再配列に関する理論的研究を行った。(1)銅酸化物高温超伝導においてCu-O鎖の再配列銅酸化物高温超伝導においてCu-O鎖の再
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配列に対するクラスターモデルを用いて量子化学計算を行った結果、酸素イオンが直線上に再配列した場合は準安定状態になることが分かった。この酸素イオンの再配列に伴いCuO_2平面の電子(セル当たり0.3電子)がCuO鎖面に遷移して、CuO_2平面のホールが増加したことになる。以上の結果から酸素イオンの準安定状態への再配列に伴い、CuO_2平面中の電子の減少が起り、超伝導転移温度の上昇が起るという機構の可能性を示すことに成功した。(2)Cu-O鎖の再配列のレーザ制御シミュレーション前述の酸素イオン再配列に対する準安定状態計算で得られたポテンシャルを用いて酸素イオン再配列のレーザー制御の可能性を示した。誘導ラマン断熱通過法(STIRAP)を用いた酸素イオン再配列のレーザー制御のためのパルス列を求めた。このレーザー制御シミュレーションから100nmの結晶薄膜を仮定すると約10^9W/cm^2のオーダーのパルスレーザーが必要であることがわかった。また従来の実験方法とは異なるCu-O鎖再配列制御の新しい可能性を示すことができた。本研究によって銅酸化物高温超伝導体における光誘起超伝導発現機構の一つである、酸素イオン再配列によるCuO_2平面のホール増加機構の可能性がはじめて示された。また酸素イオン再配列のレーザー制御の可能性が示された。今後の課題としてさらに強いレーザー照射による考察があげられる。<br />研究課題/領域番号:15035205, 研究期間(年度):2003<br />出典：「結晶におけるレーザー照射による物性発現と制御に関する理論的研究」研究成果報告書 課題番号15035205（KAKEN：科学研究費助成事業データベース（国立情報学研究所））（https://kaken.nii.ac.jp/ja/grant/KAKENHI-PROJECT-15035205/)を加工して作成
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| 22.
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長尾, 秀実 ; Nagao, Hidemi
概要:
金沢大学理工研究域数物科学系<br />光化学反応における電子伝達体の会合解離過程と拡散過程を理論的に解析し次の主な結果を得た。(1)全原子分子動力学シミュレーションからプラストシアニンとシトクロムfの酸化還元反応に関わる自由エネルギープロ
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ファイルを算出した。プラストシアニンからシトクロムfへの電子移動のポテンシャル障壁はほとんどないと結論できた。(2)タンパク質間相互作用を取り入れた新しい粗視化モデルを提案した。粗視化モデル解析から両タンパク質の活性部位間距離と電子移動反応係数に正の相関を見出した。(3)光照射下の電子伝達体の拡散過程の解析からチラコイドルーメンの膜タンパク質による障害が反応活性増減の一つの要因となると示唆できた。<br />The association/dissociation process of the electron carriers in photosynthesis has been theoretically and numerically investigated in relation to the diffusion of the proteins. The following main results have been obtained in this study. (1) Free energy profile of plastocyanin, which is one of carriers to bring one electron to cytochrome f, has been calculated by all-atom molecular dynamics simulations. The result suggests that there is no potential barrier for the electron transfer. (2) A novel coarse-grained model describing intermolecular interactions has been proposed, and the results by simulations suggest the positive correlation between the distance between the active sites and the reaction coefficient of the electron transfer. (3) Some simulations for the diffusion of plastocyanin inside the thylakoid lumen suggest that the obstacle by membrane proteins in thylakoid membrane for the electron carrier contribute to the decrease of the activity of the electron transfer.<br />研究課題/領域番号:26400429, 研究期間(年度):2014-04-01 - 2018-03-31
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| 23.
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長尾, 秀実 ; Nagao, Hidemi
概要:
二原子分子や脂質ミセルの振動モデル分子を構築し、溶媒中のモデル分子のシミュレーションを実施した。低密度溶媒中の分子間では引き込み現象は観測できなかったが、高密度溶媒中の二分子間では引き込み現象が誘発されることが分かった。以上の結果から分子振
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動の引き込み現象は高密度の溶媒中で誘起される可能性が高いことが示すことができた。今後の課題として溶媒の粘性や物性と分子の引き込み現象に関する研究が挙げられる。<br />We have discussed the dynamics of molecular systems by using some molecular models in relation to the frequency entrainment. We have found that the frequency entrainment in molecules is not observed in the solvent with lower density. On the other hand, in the case of higher density of the solvent, we have observed the frequency entrainment between molecules explicitly.<br />研究課題/領域番号:23655101, 研究期間(年度):2011-2012
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| 24.
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長尾, 秀実 ; Nagao, Hidemi
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本研究において、MgB_2超伝導体に代表される多重ギャップ超伝導発現には複数フェルミ面が重要であるという観点から、複数バンドからなる複数フェルミ面がもたらす物性発現機構を理論的に探究することを主眼に研究を行った。本研究では、(1)超伝導にお
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ける多重バンド効果のさらなる解明、(2)多重バンド効果による磁性発現の可能性、(3)有機分子性結晶における分子配向による多重バンド効果発現法則の探索、を行うことが目的である。この複数フェルミ面がもたらす新規な物性発現効果に対する理論的考察を行い、結晶構造の違いによる多重バンド効果の理論的予測を行った。超伝導発現における多重バンド効果では、多重バンド超伝導状態が単一バンド超伝導より安定化することが理論的に示された。この結果から超伝導転移温度の上昇が予測された。電子-格子相互作用による超伝導発現の場合、バンド間電子対トンネルが小さい場合は二つの異なる超伝導ギャップが存在し、バンド間対トンネルが大きい場合は区別が付かないことが示された。また、単一バンド理論の枠組みでは超伝導が発現する場合は有効電子間相互作用が引力で無ければならないが、フェルミ面が二つのバンドを横切る場合は斥力電子間相互作用でも超伝導発現することが示された。磁性における多重バンド効果では、二重バンド構造と磁性についての理論的考察を行った。単一バンド理論に相当するフェルミ面が1つのバンドを横切る場合は反強磁性的であるのに対し、フェルミ面が2つのバンドを横切る場合にはhalf-filling近傍で強磁性的になる可能性を示すことができた。有機分子性結晶の多くに見られるヘリーンボーン構造と二層正方格子構造についての物性発現予測を行った結果、二層正方格子構造では多重バンド効果により新規な磁性および超伝導性発現の可能性があることが示された。また、外場下での物性変化についても考察を行った。<br />Many bands play an important role of many gap superconductivity such as MgB_2 superconductor. Form viewpoint of the importance of many-band, we have theoretically investigated new physical properties such as superconducting gaps etc. arising from many-band. Our purposes of this project are (1) to investigate many-band effects on superconductivity, (2) to investigate many-band effects on magnetism and to discuss the possibility of new magnetic properties, and (3) to investigate many-band effects in molecular crystals. In this project, we have investigated many-band effects on superconductivity and magnetism by using Green's function techniques and some many-band models.In many-band effects on superconductivity, we have obtained that the superconducting gap in namy-band systems becomes more stable than that of single band systems. The transition temperature for many-band superconductivity becomes higher than that of single band superconductivity. An effective two-electron pair scattering process between bands has a very important role to apper many-band superconductivity. We also have investigated a cooperative mechanism for superconductivity with the pair electron scattering process and the effective electron interactins from electron-phonon interaction. In a single band model such as BCS model, the effective electron interaction should be negative. However, In many-band systems, many-band superconductivity appears, even if the effective electron interaction becomes positive or negative.In many-band effects on magnetism, we have found that effective electron-electron interaction becomes ferromagnetic at half-filling in many-band systems and that antiferromagnetic interaction appears by hole-doping into the many-band systems.We have investigated magnetic and superconducting properties of herringbone and two-layer square lattices in organic crystals. In the two-layer square lattice, we have obtained that we can expect interesting magnetic properties by many-band effects and have also found the possibilities of many-band superconductivity in such two-layer lattices.<br />研究課題/領域番号:15550010, 研究期間(年度):2003-2004<br />出典：「分子性結晶構造と超伝導および磁性における多重バンド効果の関連性に関する理論的研究」研究成果報告書 課題番号15550010 (KAKEN：科学研究費助成事業データベース（国立情報学研究所）) 本文データは著者版報告書より作成
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| 25.
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長尾, 秀実 ; Nagao, Hidemi
概要:
金沢大学理工研究域<br />本研究では分子性結晶における超伝導発現および外場誘導超伝導発現の可能性についての理論的研究を行った。まずはじめに、電子-格子相互作用をによるバンド内有効電子間相互作用と電子対散乱あるいは電子対トンネルを含むバン
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ド間有効電子間相互作用に着目し、平均場近似、二粒子グリーン関数法、繰り込み郡の方法などを用いて超伝導状態について理論的に考察を行い、以下の結果を得た。フェルミ面が複数のバンドを横切る場合には超伝導における多重バンド効果が起ることが理論的に示された。超伝導の多重バンド効果により超伝導ギャップが安定化して、超伝導転移温度がより高くなることが示された。このような多重バンド超伝導では電子間相互作用により単数あるいは複数の超伝導ギャップが現われることが示された。次に、平均場近似レベルでの超伝導状態計算プログラムを開発し、有機分子性結晶などのへの展開も試みた。有機分子結晶の多くに見られるヘリンボーン構造をみると二重バンド構造を持つことが分かる。このバンド構造への電子あるいはホールドープが可能であれば、超伝導発現の可能性が期待されることが示された。また、有効電子間相互作用の対称性と超伝導ギャップの対称性の関連性が示された。これらの計算から、多層構造をもつ有機分子性結晶では外場誘導超伝導の可能性が期待される。一方、外場誘導超伝導実現は外場による格子歪みなどの問題があり、今後の課題である。現在、これらのプログラムの第一原理計算への拡張を展開している。<br />研究課題/領域番号:13740328, 研究期間(年度):2001-2002<br />出典：「有機分子性結晶の外場誘導超伝導発現の理論的研究」研究成果報告書 課題番号13740328（KAKEN：科学研究費助成事業データベース（国立情報学研究所））（ https://kaken.nii.ac.jp/ja/grant/KAKENHI-PROJECT-13740328/）を加工して作成
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