Tinker‐OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU‐based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker‐OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200‐fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host–guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. © 2017 Wiley Periodicals, Inc.     

A new type of microemulsion containing task-special ionic liquid [NH2ebim][BF4]

The formation of microemulsions in the presence of cyclohexane, Triton X-100, n-butanol, water, and task-special ionic liquid (TSIL) (1-2-aminoethyl-3-butylimidazolium tetrafluoroborate) was studied at 25°C. The phase behavior of this ternary system was investigated. Three subregions (namely, water-in-oil phase, bicontinuous phase, and oil-in-water phase) were identified in the single-phase region by dynamic light scattering (DLS) technique and electrical conductivity measurement. Microstructures of microemulsions with different water contents have been predicted by using dissipative particle dynamics (DPD) simulation. It was found that the DPD simulations successfully reproduce the experimental results in the article. The location of TSIL in the microemulsions was predicted by DPD simulation further. The result indicates that TSIL is more easy to locate in the surfactant and cosurfactant layer and has amphiphilicity, which provides us new insights into the potential applications of TSIL-based microemulsions in separation and new nano-scale material preparation because of the interaction of TSIL with some special components at the interface of oil and water.     

量子点荧光印迹传感器的计算机模拟设计、制备及检测河水中4-硝基苯酚的应用

将量子点的荧光特性、表面分子印迹技术与计算机模拟技术相结合,分别以碲化镉、4-硝基苯酚、3-氨丙基三乙氧基硅烷和正硅酸四乙酯作为量子点、模板分子、功能单体和交联剂,制得具有荧光特性的分子印迹聚合物.对其结构、形貌、荧光性能和选择性进行了表征,结果表明,该聚合物对4-硝基苯酚具有良好的选择性和灵敏度,线性范围为1.0~80 nmol/m L,检出限为0.05 nmol/m L.将制备的量子点荧光印迹聚合物作为传感器,应用于河水中4-硝基苯酚的测定,加标回收率为98.6%~101.2%,相对标准偏差最高为1.37%.     

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.     

Phase behavior and interfacial properties of diblock copolymer-homopolymer ternary mixtures: Influence of volume fraction of copolymers and interaction energy

We use a Monte Carlo method to study the phase and interfacial behaviors of A-b-B diblocks in a blend of homopolymers, A and B, which are confined between two asymmetric hard and impenetrable walls. Our results show that, when the interaction strength is weak, the block copolymersare uniformly distributed in the ternary mixtures under considered concentrations. Under strong interaction strength, distribution region of the block copolymers changes from a single smooth interface to a curved interface or multi-layer interface in the ternary mixtures. Furthermore, our findings show that with increasing volume fraction of A-b-B diblock copolymer(фC), copolymer profiles broaden while фC≥ 0.4, a lamellar phase is formed and by further increasing фC, more thinner layers are observed. Moreover, the results show that, with the increase of фC, the phase interface first gradually transforms from plane to a curved surface rather than micelle or lamellar phase while with the increase of the interaction between A and B segments(ε_(AB)), the copolymer chains not only get stretched in the direction perpendicular to the interface, but also are oriented. The simulations also revealthat the difference between symmetric and asymmetric copolymers is negligible in statistics if the lengths of two blocksare comparable.     

高速碰撞中的有限元方法及其应用

讨论了连续介质力学守恒方程的有限元离散方法,针对高速碰撞的物理特点,提出了数值计算中所应重视的问题及其有效的解决办法。文中给出的典型算例说明本方法对各类高速碰撞问题的数值模拟计算是十分有用和成功的。     

基于MATLAB的GPS软件接收机捕获与跟踪算法实现

研究了GPS软件接收机的捕获和跟踪算法,并基于Matlab软件平台和射频前端在PC上实现了GPS软件接收机样机。介绍了GPS软件接收机的结构和数据采集硬件,讨论了GPSC/A码的特性、产生原理以及捕获过程。针对传统的串行搜索算法慢的缺点以及高动态GPS软件接收机的特点,在该样机中实现了快速的基于循环卷积的并行捕获算法,并联合使用超前滞后环和对相位反转不敏感的科斯塔斯锁相环分别对码相位和多普勒频偏进行跟踪,解调得到导航电文。仿真和测试结果表明,使用GPS软件接收机进行信号处理的思想使用户在算法处理和软件升级等方面具有更大的灵活性,可应用于下一代任何全球导航卫星定位系统(GNSS)和空基增强系统(SBAS)接收机的设计。     

On the determination of the Young’s modulus of thin films using indentation tests

The main difficulty with the characterization of thin coatings using depth-sensing indentation tests is related to the determination of the contributions of the substrate and the film to the measured properties. In this study, three-dimensional numerical simulations of the Vickers hardness test are used in order to examine the influence of the elastic and plastic properties of the substrate and the film on the composite’s Young’s modulus results. The hardness of the film is equal to or higher than the substrate hardness. A study of the stress distributions and the indentation geometry of composites, film/substrate, was performed, taking into account the relative mechanical properties of the film and substrate. In addition, stress evolution during indentation was studied, in order to quantify the critical indentation depth under which the substrate is not elastically deformed. The accurate evaluation of the Young’s modulus of the films using weight functions is also examined: some of these have previously been proposed and one was introduced for this study. Two different fitting procedures were used to compare the results obtained from eight fictive film/substrate combinations using six weight functions. The first procedure, commonly used, considers the substrate’s modulus as a known parameter in the fitting process. In the second, the film and the substrate’s modulus are considered as unknown variables that are calculated simultaneously during the fitting process. The validity of the conclusions obtained using the fictive materials was checked by applying the weight functions to four real composites.