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A Noniterative mean-field QM/MM-type approach with a linear response approximation toward an efficient free-energy evaluation

城戸 健太朗

Journal of Computational Chemistry, 40(24), p.2072 - 2085, 2019/09

 被引用回数:1 パーセンタイル:78.85(Chemistry, Multidisciplinary)

Mean-field treatment of solvent provides an efficient technique to investigate chemical processes in solution in QM/MM framework. In the algorithm, an iterative calculation is required to obtain the self-consistency between QM and MM regions, which is a time-consuming step. In the present study, we have proposed a non-iterative approach by introducing a linear response approximation (LRA) into the solvation term in the one-electron part of Fock matrix in a hybrid approach between MO calculations and a three-dimensional integral equation theory for molecular liquids (MC-MOZ-SCF; Kido $textit{et al.}$, J. Chem. Phys. $textbf{143}$, 014103 (2015)). To save the computational time, we have also developed a fast method to generate electrostatic potential map near solute and the solvation term in Fock matrix, using Fourier transformation (FT) and real spherical harmonics expansion (RSHE). To numerically validate the LRA and FT-RSHE method, we applied the present approach to water, carbonic acid and their ionic species in aqueous solution. Molecular properties of the solutes were evaluated by the present approach with four different types of initial wave function and compared with those by the original (MC-MOZ-SCF). From the averaged speed up ratio, the present approach is 13.5 times faster than MC-MOZ-SCF.


ERmod; Fast and versatile computation software for solvation free energy with approximate theory of solutions

櫻庭 俊; 松林 伸幸*

Journal of Computational Chemistry, 35(21), p.1592 - 1608, 2014/08

 被引用回数:38 パーセンタイル:21.12(Chemistry, Multidisciplinary)



Adaptive lambda square dynamics simulation; An Efficient conformational sampling method for biomolecules

池部 仁善; 櫻庭 俊; 河野 秀俊

Journal of Computational Chemistry, 35(1), p.39 - 50, 2014/01

 被引用回数:13 パーセンタイル:50.93(Chemistry, Multidisciplinary)

A novel, efficient sampling method for biomolecules is proposed. The partial McMD was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for poly-lysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems.


A Possible overestimation of the effect of acetylation on lysin residues in KQ mutant analysis

藤本 浩文*; 樋口 真理子; 小池 学*; 大出 裕高*; Pinak, M.; Kotulic Bunta, J.*; 根本 俊行*; 作道 隆*; 本田 尚子*; 前川 秀彰*; et al.

Journal of Computational Chemistry, 33(3), p.239 - 246, 2012/01

 被引用回数:18 パーセンタイル:44.19(Chemistry, Multidisciplinary)



Branch migration of Holliday junction in RuvA tetramer complex studied by umbrella sampling simulation using a path-search algorithm

石田 恒

Journal of Computational Chemistry, 31(12), p.2317 - 2329, 2010/09

Branch migration of the Holliday junction takes place at the center of the RuvA tetramer. To elucidate how branch migration occurs, umbrella sampling simulations were performed for complexes of the RuvA tetramer and Holliday junction DNA. While conventional umbrella sampling simulations set sampling points a priori, the umbrella sampling simulation in this study set the sampling points one by one in order to search for a realistic path of the branch migration during the simulations. Starting from the X-ray structure of the complex, in which the hydrogen bonds between two base-pairs were unformed, the hydrogen bonds between the next base-pairs of the shrinking stems were observed to start to disconnect. At the intermediate stage, three or four of the eight unpaired bases interacted closely with the acidic pins from RuvA. During the final stage, these bases moved away from the pins and formed the hydrogen bonds of the new base-pairs of the growing stems. The free-energy profile along this reaction path showed that the intermediate stage was ameta-stable state between two free-energy barriers of about 10-15 kcal/mol. These results imply that the pins play an important role in stabilizing the interactions between the pins and the unpaired base-pairs.


Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site

藤本 浩文*; Pinak, M.; 根本 俊行*; O'Neill, P.*; 久米 悦雄; 斎藤 公明; 前川 秀明*

Journal of Computational Chemistry, 26(8), p.788 - 798, 2005/06

 被引用回数:22 パーセンタイル:43.32(Chemistry, Multidisciplinary)

電離放射線によるDNAクラスター損傷は修復され難く、細胞のガン化など生体にとって深刻な事態を引き起こす原因の一つと考えられている。DNAクラスター損傷を持つDNA分子には、単独の損傷を持つ分子と比べるとDNA修復酵素が作用し難いことが、生化学的・分子生物学的実験によって示されているが、どのような要因が酵素の作用阻害に関わっているかはいまだ不明である。そこで本研究では、DNAクラスター損傷における酵素の作用阻害の要因を、計算科学的手法を用いて考察した。既報の実験で用いられたDNA分子と同配列となるように、7,8-dihydro-8-oxoguanine(8-oxoG)及びapurinic/apyrimidinic(AP) siteという2つの酸化損傷部位が数塩基はなれた位置に存在する40merのDNA分子を、2損傷部位間の距離を変えて6種類設計し、それぞれに対し分子動力学的(MD)シミュレーションを1nsのオーダーで行った。その結果、損傷部位における分子の屈曲や、損傷塩基と相補鎖上の塩基との相互静電エネルギーの減少など損傷DNA分子に特徴的な構造や性質が観察された。これらの特徴によって修復酵素がDNAに結合できず、したがって修復効率が低下したのではないかと推察される。


8-oxoguanine lesioned B-DNA molecule complexed with repair enzyme hOGG1; A Molecular dynamics study

Pinak, M.

Journal of Computational Chemistry, 24(7), p.898 - 907, 2003/04

 被引用回数:8 パーセンタイル:62.22(Chemistry, Multidisciplinary)



Molecular dynamics simulation of thymine glycol-lesioned DNA reveals specific hydration at the lesion

Pinak, M.

Journal of Computational Chemistry, 22(15), p.1723 - 1731, 2001/11

 被引用回数:3 パーセンタイル:77.31(Chemistry, Multidisciplinary)


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