Dynamical Emergence Principle of Reaction Selectivity and Molecular Memory in Chemical Reactions' and Biomolecular Systems

化学反应和生物分子系统中反应选择性和分子记忆的动态涌现原理

• 批准号: 15540394
• 负责人: KOMATSUZAKI Tamiki
• 金额: $ 2.18万
• 依托单位: Kobe University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2003
• 资助国家: 日本
• 起止时间: 2003 至 2005
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-15540394/
• 关键词: Chemical Reaction Dynamics; Normally hyperbolic invariant manifold; Dynamical Systems; Phase space geometry; Normal form theory; Transition state; たんぱく質ダイナミックス; 多遷移過程; 次元縮約性とエネルギー地形; 相空間の幾何学; ダイナミックスの階層性

No-return transition states (TSs) defined in multidimensional phase space, where recrossing trajectories through the commonly used ‘configuration' TS pass only once, robustly exist up to moderately high energy regime above the reaction threshold even when nonlinear resonances among the bath degrees of freedom perpendicular to the reaction coordinate result in local chaos. However, at much higher energy when global chaos appears in the bath space, the separability of the reaction coordinate from the bath degrees of freedom ceases to hold locally. In the phase space near the saddles, it is found that the slower the system passes the TS, the more recrossing trajectories reappear. Their implications and mechanisms are discussed concerning to what extent one can define no-return TSs in high energy regime above the reaction threshold.We also developed a new empirical self-consistent scheme to elucidate the local ergodic state distribution function and construct effective multidimensional free energy landscape from an ensemble of short single molecule time series. It is possible to capture not the entire topography of the multidimensional free energy landscape but the regions where the system wanders frequently. Using local ergodicity ansatz as a 0^<th> order description, we constructed the multidimensional "free energy" landscape where several local ergodic states are linked with introducing a "distance" among them. Evaluating on the probability of transition sequences sampled in an ensemble of single molecule time series, one can analyze non-Markovianity along several transition paths. e.g., relationship between memory and length of transition paths. As a function of n_s time window to estimate the short time distribution, we can also assign the number of accessible superbasins (a set of states) within time n_s.

定义在多维相空间中的不返回过渡态(TSS)，其中穿过常用的“构型”TS的轨迹只通过一次，即使当垂直于反应坐标的浴场自由度之间的非线性共振导致局部混沌时，TSS仍然强健地存在到反应阈值以上的中等高能区。然而，在更高的能量下，当浴场空间出现整体混沌时，反应坐标与浴场自由度的可分性在局部不再成立。在鞍点附近的相空间中，系统通过TS的速度越慢，重新出现的轨迹就越多。我们还发展了一个新的经验自洽方案来解释局域遍历态分布函数，并从短的单分子时间序列中构造有效的多维自由能景观。有可能捕捉到的不是多维自由能景观的整个地形，而是系统频繁漂移的区域。利用局域遍历性ansatz作为0阶描述，我们构造了多维“自由能”景观，其中几个局域遍历态通过引入“距离”而联系在一起。对单分子时间序列集合中抽样的转变序列的概率进行评估，可以分析沿几条转变路径的非马尔可夫性。例如存储器和转换路径长度之间的关系。作为估计短时间分布的n_S时间窗的函数，我们也可以指定在n_S时间内可到达的超盆地(一组状态)的数目。

项目成果

Regularity in chaotic transitions on multibasin landscapes

多流域景观混沌转变的规律性

• 发表时间: 2005
• 期刊: Advances in Chemical Physics 第130B巻
• 作者: 富松 裕;大原 雅;N.Saito;M.Okubo;M.Okubo;N.Saito;N.Saito;渡部 鉄兵;渡部 鉄兵;渡辺 鉄兵;Chun-Biu Li;小松崎 民樹
• 通讯作者: 小松崎 民樹

Phase-space reaction network on a multisaddle energy landscape: HCN isomerization.

• DOI: 10.1063/1.2044707
• 发表时间: 2005-11
• 期刊: The Journal of chemical physics
• 作者: Chun-Biu Li;Y. Matsunaga;M. Toda;T. Komatsuzaki

Yasuhiro Matsunaga: "Protein Folding Dynamics : Ergodic Behavior in Principal Component Space"AIP conference series for Slow Dynamics in Complex Systems. (発表予定). 2 (2004)

Yasuhiro Matsunaga：“蛋白质折叠动力学：主成分空间中的遍历行为”AIP 复杂系统慢动力学会议系列（即将发表）。

水の場としての集団運動と生体分子の構造転移ダイナミックス

水场的集体运动和生物分子的结构转变动力学

• 发表时间: 2006
• 期刊: 物性研究 86
• 作者: S.Komura;N.Shimokawa;T.Kato;納多哲史
• 通讯作者: 納多哲史

Regularity in Chaotic Transitions on Two-Basin Lands

两盆土地上混沌转变的规律性

• 发表时间: 2005
• 期刊: Advances in Chemical Physics 130 A
• 作者: K.Hoshino;Y.Matsunaga;Gareth J.Rylance;Roy L.Johnston;D.J.Wales;Tamiki Komatsuzaki;Tamiki Komatsuzaki
• 通讯作者: Tamiki Komatsuzaki