固体塑性实验室时间尺度的分子动力学模拟概述

随着超级计算机软硬件的飞速提升,基于经验势函数的分子动力学模拟在解析固体塑性的微观机制方面发挥着关键作用。但是,由于传统分子动力学基于牛顿运动方程数值积分,积分时间步长通常为飞秒量级,其模拟的时间尺度通常限于纳秒量级,从而为模拟长时间尺度固体塑性机制带来了巨大的挑战。本文从分子动力学模拟的时间尺度限制切入,介绍目前国际流行的几种实验室时间尺度原子模拟技术,并以晶体位错塑性与非晶态物质扩散和剪切转变塑性为例,阐述实验室时间尺度和原子精度计算机模拟的思想与实施步骤。最后,展望了目前加速分子动力学方法普遍存在的问题,并提出可能的解决方案。

白腐菌漆酶耐盐性的生物信息学研究及氯离子、氧气和水分子输运通道分析

运用生物信息学方法分析了各物种漆酶的耐盐性差异,并利用随机加速动力学模拟计算揭示了白腐菌漆酶内部连接三铜活性中心(TNC)的氯离子、氧气和水分子的可能输运通路.生物信息学系统发生树和结构比对分析表明,担子真菌、子囊真菌与细菌漆酶具有较高的结构保守性;通过随机加速动力学模拟发现,白腐菌T.versicolor漆酶内部有5条小分子输运通道(p1~p5),其中p2和p5为新的输运通道;与氧气和水分子输运不同,氯离子在漆酶内部输运时受到明显约束,以较高的几率通过p1和p4输运通道.高耐盐漆酶的p1通道周边富集了更多酸性和芳香性氨基酸残基,降低了氯离子的输运效率,从而提高其耐盐性.

Characterization of the dissociation pathways of dichloromethane and glutathione in dichloromethane dehalogenase

Dichloromethane(DCM)dehalogenase stands as a crucial enzyme implicated in the degradation of methylene chloride across diverse environmental and biological contexts.However,the unbinding pathways of ligands from DCM dehalogenase remain unexplored.In order to gain a deeper understanding of the binding sites and dissociation pathways of dichloromethane(DCM)and glutathione(GSH)from the DCM dehalogenase,random accelerated molecular dynamics(RAMD)simulations were performed,in which DCM and GSH were forced to leave the active site.The protein structure was predicted using Alphafold2,and the conformations of GSH and DCM in the binding pocket were predicted by docking.A long equilibrium simulation was conducted to validate the structure of the complex.The results show that GSH is most commonly observed in three main pathways,one of which is more important than the other two.In addition,DCM was observed to escape along a unique pathway.The key residues and protein helices of each pathway were identified.The results can provide a theoretical foundation for the subsequent dissociation mechanism of DCM dehalogenase.

基于Burgers向量提取与分析的改进PRD算法在位错环模拟中的应用

RAFM钢经中子辐照后会产生两种类型的间隙位错环(1/2〈111〉环和〈100〉环),导致长时间服役后出现辐照硬化与脆化现象,因此理清不同类型位错环的形成与转变过程对材料微结构演化及性能预测具有重要意义。本文基于加速分子动力学中的并行副本复制法(PRD),通过分析位错环转变的机理特性,提取Burgers向量,改进了PRD在位错环模拟上的应用,实现了〈100〉环向1/2〈111〉环的加速转变现象模拟。结果表明:在1000 K下,采用改进PRD算法程序进行模拟,小尺寸〈100〉环会发生向1/2〈111〉环的转变,转变时间比传统分子动力学方法更快;大尺寸〈100〉环会出现〈100〉位错段和1/2〈111〉位错段共存的状态,甚至在带有Ni溶质元素的〈100〉环中还发现了完全转变到1/2〈111〉位错环的现象。此外,对程序模拟的准确性进行验证并分析评估了加速性能与并行性能,通过与原PRD算法对比,发现其并行效率远高于原PRD,并行效率在90%左右,且并行规模的增加对于并行性的影响不大,可以很好地进行大规模并行扩展。

喹啉加氧酶中氧气扩散的通道分析

通过生物信息学分析、量化计算优化、CAVER和MDpocket预测、随机加速分子动力学及伞状抽样动力学模拟等方法,对喹啉加氧酶(HOD)中的氧气扩散途径进行了计算预测.结果表明,氧气在HOD中的反应位点包埋在蛋白内部,而HOD中有数条可能的通道供氧气进出,其中长度最短的通道具有最高的优先度,不仅在随机加速动力学模拟中具有最高的氧气逸出概率,而且伞状抽样方法计算得到的自由能也最低.此通道的内端位于底物Re面的氧气结合位点,较好地解释了HOD的相关实验数据.

Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules

Molecular dynamics simulation has emerged as a powerful computational tool for studying biomolecules as it can provide atomic insights into the conformational transitions involved in biological functions.However,when applied to complex biological macromolecules,the conformational sampling ability of conventional molecular dynamics is limited by the rugged free energy landscapes,leading to inherent timescale gaps between molecular dynamics simulations and real biological processes.To address this issue,several advanced enhanced sampling methods have been proposed to improve the sampling efficiency in molecular dynamics.In this review,the theoretical basis,practical applications,and recent improvements of both constraint and unconstrained enhanced sampling methods are summarized.Furthermore,the combined utilizations of different enhanced sampling methods that take advantage of both approaches are also briefly discussed.

Molecular dynamics analysis on bending mechanical behavior of alumina nanowires at different loading rates

The molecular dynamics(MD)model ofα-Al_(2)O_(3) nanowires in bending is established by using LAMMPS to calculate the atomic stress and strain at different loading rates in order to study the effect of loading rate on the bending mechanical behaviors of theα-Al_(2)O_(3) nanowires.Research results show that the maximum surface stress−rotation angle curves ofα-Al_(2)O_(3) nanowires at different loading rates are all divided into three stages of elastic deformation,plastic deformation and failure,where the elastic limit point can be determined by the curve symmetry during loading and unloading cycle.The loading rate has great influence on the plastic deformation but little on the elastic modulus ofα-Al_(2)O_(3) nanowires.When the loading rate is increased,the plastic deformation stage is shortened and the material is easier to fail in brittle fracture.Therefore,the elastic limit and the strength limit(determined by the direct and indirect MD simulation methods)are closer to each other.The MD simulation result ofα-Al_(2)O_(3) nanowires is verified to be valid by the good agreement with the improved loop test results.The direct MD method becomes an effective way to determine the elastic limit and the strength limit of nanoscale whiskers failed in brittle or ductile fracture at arbitrary loading rate.

重要性采样方法与自由能计算

分子动力学模拟与自由能计算已经在化学、生物学与材料学等领域得到广泛的应用。然而,由于在传统分子动力学模拟的时间尺度内,体系很难跨越较高的自由能能垒,在相空间内的采样大大受限,采样困难使自由能计算难以收敛。增强采样是解决这一问题的有效途径,重要性采样方法就是其中一类。本文综述了四种广泛应用的重要性采样方法——伞状采样方法、metadynamics方法、自适应偏置力方法和温度加速分子动力学方法的原理和进展,其中重点概述了自适应偏置力方法的最新发展——扩展自适应偏置力方法和扩展广义自适应偏置力方法,并对这四种重要性采样方法的优缺点进行了比较。最后,讨论和展望了重要性采样与自由能计算方法面临的挑战和前景,并提出了对自适应偏置力方法可能的改进,如与加速分子动力学(aMD)或弦方法结合以提高在高维度空间中的采样效率。

MD simulations of loading rate dependence of detwinning deformation in nanocrystalline Ni

Molecular dynamics simulations are performed to investigate the deformation behavior of nanocrystalline Ni with pre-twin atom structure.The simulation sample is composed of four grains with average size 12 nm.The simulation technique of isobaric-isothermal ensemble(NPT) with high pressure is applied to obtain a sample with two circle twins.Under uniaxial tensile and shear loading,as well as different detwinning deformation behaviors are observed.Under uniaxial tension the detwinning deformation is induced by the event of grain growth,and it is supported by local energy analysis.Under the shear loading the detwinning deformation is related to the loading rate.The results show that there may be a critical shear rate.As the shear rate is sufficiently high the circle twin is found to be failed;as the shear rate is less than that rate,the size of circle twin become smaller and gradually approach a constant value.Our simulation results are in good agreement with experiment observation.

Chip formation dependence of machining velocities in nano-scale by molecular dynamics simulations

In this study, molecular dynamics simulations were carried out to study the effect of machining velocities on the mechanism of chip formation in nano-metric copper. A wide range of cutting velocities was performed from 10 to 2000 m/s, and the microstructure's evolution from a crystalline state to an amorphous state was studied. At the low machining velocity, dislocations were generated from the surface in front of the tool, and the immobile dislocation deduced by the cross slip of dislocation was observed. At the high machining velocity, no crystal dislocation nucleated, but instead disorder atoms were found near the tool. Temperature near the tool region increased with the increasing machining velocities, and the temperature had an important effect on the phase transition of the crystal structure.