Quantum reaction dynamics of C(1D) + HD → CH(CD) + D(H) on the ground state potential energy surface

We present accurate quantum dynamic calculations of the reaction C(¹D) + HD on the latest version of the potential energy surface [Zhang et al., J. Chem. Phys. 140, 234301 (2014)]. Using a Chebyshev real wave packet method with full Coriolis coupling, we obtain the initial state‐specified ( ) reaction probabilities, integral cross sections, and rate constants. The resulting probabilities display oscillatory structures due to numerous long‐lived resonances supported by the deep potential well. The calculated rate constants and CD/CH product branching ratio at room temperature are in reasonably good agreement with the experimental measurements.     

Temperature‐shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins

Parallel cascade selection molecular dynamics (PaCS‐MD) is an enhanced conformational sampling method for searching structural transition pathways from a given reactant to a product. Recently, a temperature‐aided PaCS‐MD (Vinod et al., Eur. Biophys. J. 2016, 45, 463) has been proposed as its extension, in which the temperatures were introduced as additional parameters in conformational resampling, whereas the temperature is fixed in the original PaCS‐MD. In the present study, temperature‐shuffled PaCS‐MD is proposed as a further extension of temperature‐aided PaCS‐MD in which the temperatures are shuffled among different replicas at the beginning of each cycle of conformational resampling. To evaluate their conformational sampling efficiencies, the original, temperature‐aided, and temperature‐shuffled PaCS‐MD were applied to a protein‐folding process of Trp‐cage, and their minimum computational costs to identify the native state were addressed. Through the evaluation, it was confirmed that temperature‐shuffled PaCS‐MD remarkably accelerated the protein‐folding process of Trp‐cage compared with the other methods. © 2017 Wiley Periodicals, Inc.     

Analysis of droplet behavior in a de-oiling hydrocyclone

A mechanical separation process in a de-oiling hydrocyclone is described in which disperse oil droplets are separated from a continuous water phase. This separation process is influenced by droplet breakage and coalescence. Based on experimental data and simulation results in a stirred tank, a modified breakage model, which can be applied to droplet breakage in the de-oiling hydrocyclone, is developed. Then, a simulation model is developed coupling the numerical solution of the flow field in the hydrocyclone based on computational fluid dynamics (CFD) with population balances. The homogenous discrete method and the inhomogeneous discrete method are applied for solving the population balance model (PBM). The investigations show that the numerical results obtained by the simulation model coupled with the modified PBM using the inhomogeneous discrete method are in good accordance with experimental data under a high flow rate. According to this simulation model, the effect of three different inlet designs on the separation efficiency of the de-oiling hydrocyclone has been discussed. The results indicate that the separation efficiency of the de-oiling hydrocyclone can be improved with an appropriate inlet design.     

Structural dissimilarity sampling with dynamically self‐guiding selection

Structural dissimilarity sampling (SDS) has been proposed as an enhanced conformational sampling method for reproducing the structural transitions of a given protein. SDS consists of cycles of two steps: (1) Selections of initial structures with structural dissimilarities by referring to a measure. (2) Conformational resampling by restarting short‐time molecular dynamics (MD) simulations from the initial structures. In the present study, an efficient measure is proposed as a dynamically self‐guiding selection to accelerate the structural transitions from a reactant state to a product state as an extension to the original SDS. In the extended SDS, the inner product (IP ) between the reactant and the snapshots generated by short‐time MD simulations are evaluated and ranked according to the IP s at every cycle. Then, the snapshots with low IP s are selected as initial structures for the short‐time MD simulations. This scheme enables one to choose dissimilar and distant initial structures from the reactant, and thus the initial structures dynamically head towards the product, promoting structural transitions from the reactant. To confirm the conformational sampling efficiency, the extended SDS was applied to maltodextrin binding protein (MBP), and we successfully reproduced the structural transition from the open to closed states with submicrosecond‐order simulation times. However, a conventional long‐time MD simulation failed to reproduce the same structural transition. We also compared the performance with that obtained by the ordinary SDS and other sampling techniques that have been developed by us to characterize the possible utility of the extended SDS for actual applications. © 2017 Wiley Periodicals, Inc.     

N-脒基脲二硝酰胺盐晶体形貌的分子动力学研究

采用分子动力学方法,在正侧(NVT)系综下研究了N-脒基脲二硝酰胺盐(FOX-12)在溶剂中的晶体形貌.通过构建溶剂分子层-晶面的界面吸附模型模拟其动力学平衡构型,计算溶剂与晶体表面间的结合能,进而对真空附着能进行修正并获得溶剂条件下的晶貌.使用自然冷却法在水和水/甲醇中培养FOX-12晶体并利用扫描电子显微镜进行了表征.结果表明,在真空条件下决定FOX-12晶貌的6个重要晶面为(110),(200),(201),(011),(002)和(111);FOX-12在水溶液条件下的主要晶面为(110)和(011),在水/甲醇溶液条件下的主要晶面为(200)和(011),预测的晶体形貌与实验结果相吻合.对水分子和FOX-12的(110)面间的径向分布函数进行了计算,分析了水分子和晶面间的分子间作用力.     

血管紧张素转换酶与抑制肽结合模式的分子动力学研究

应用分子模拟方法研究了血管紧张素转换酶(Angiotensin-converting enzyme,ACE)C端结构域(C-domain)与两种抑制肽(RIGLF/AHEPVK)的结合机制,预测了两个体系的结合模式,提出在C-domain-RIGLF中His353,Asp377,Asp453,Phe457,His513,Tyr523和Phe527为RIGLF主要结合残基,而在C-domainAHEPVK中Gln281,His353,Ser355,Glu384,Lys511,His513和Tyr523等残基起关键作用.应用结合自由能计算比较了两个体系的结合能力,结果表明,RIGLF和AHEPVK均与C-domain活性位点残基存在较强作用,且AHEPVK对C-domain的结合能力较强,与实验结果一致.     

Analytical dynamics of continuous medium and its application

综述了国内和国外学者研究连续介质分析动力学问题的进展,阐明了本文主要论述将Lagrange方程应用于连续介质动力学的问题.论文采用Lagrange-Hamilton体系,分别论述了非保守非线性弹性动力学、不可压缩黏性流体动力学、黏弹性动力学、热弹性动力学、刚--弹耦合动力学和刚--液耦合动力学的Lagrange方程及其应用.论述了应用Lagrange方程建立有限元计算模型的问题. 最后,展望了将Lagrange方程应用于连续介质动力学问题的研究前景.     

Redundant actuators to achieve minimal vibration trajectory tracking of flexible multibodies: Theory and application

We address the problem of inverse dynamics for flexible multibodies, which arises, in trajectory tracking control of flexible multibodies such as space manipulators and articulated flexible structures. Previous research has resolved this trajectory tracking problem by computing the system inputs for feedforward control of actuators at the joints. Recently, the use of distributed actuators like electro-strictive actuators in flexible structures has introduced a new dimension to this trajectory tracking problem. In this paper we optimally utilize such actuators to aid joint actuators for tracking control, and introduce a new inverse dynamics scheme for simultaneously (1) tracking a prescribed trajectory and (2) minimizing ensuing elastic deflections. We apply this scheme for trajectory tracking of a two-link two-joint planar manipulator with joint motors and distributed electro-strictive actuators. Experimental results are presented to contrast our new scheme with other existing methods.