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居中热库蛙跳算法的大尺度模拟测试
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作者 孙兆玺 payam kalhor +1 位作者 徐扬 刘剑 《Chinese Journal of Chemical Physics》 SCIE CAS CSCD 2021年第6期932-948,I0005,共18页
分子动力学模拟一个必不可少的要素是对运动方程的准确高效积分.尽管在动力学传播框架内的现代计算工具中大量使用了传统的蛙跳算法,研究表明蛙跳算法仍然可以进一步改进以获得更好的性能.居中控温方案中蛙跳的改进版本(蛙跳-middle)实... 分子动力学模拟一个必不可少的要素是对运动方程的准确高效积分.尽管在动力学传播框架内的现代计算工具中大量使用了传统的蛙跳算法,研究表明蛙跳算法仍然可以进一步改进以获得更好的性能.居中控温方案中蛙跳的改进版本(蛙跳-middle)实现了更高的精度和效率,即使积分时间步长扩大了几倍,也能保持稳定的动力学传播.本文使用常规和增强采样模拟中对两个积分算法(蛙跳和蛙跳-middle)进行大尺度模拟测试,旨在标定由时间步长引起的全局性质(例如,详细的势能项)的变化行为以及复杂系统的实际模拟中的局部可观察量(例如,自由能变化或键长).测试集由六个化学和生物相关系统组成,包括N-甲基乙酰胺和A7-T7DNA中二面角翻转的构象变化、丙二醛内的分子内质子转移、苯和苯酚针对T4溶菌酶L99A的结合自由能计算、乙胺醇低共熔溶剂中的羟基键长变化以及蓝光受体蛋白的势能计算.所有结果显示蛙跳-middle积分算法中时间步长引起的误差较小.蛙跳-middle相对传统蛙跳积分算法的性能提高对于全局属性比局部可观测量更大.总体而言,目前的工作结果表明,在实际化学和生物系统的模拟中,应优先应用蛙跳-middle算法以获得准确的热力学行为和性质. 展开更多
关键词 分子动力学 蛙跳算法 居中热库方案
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Potassium carbonate-based ternary transition temperature mixture(deep eutectic analogues)for CO_(2)absorption:Characterizations and DFT analysis 被引量:1
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作者 Hosein Ghaedi payam kalhor +3 位作者 Ming Zhao Peter T.Clough Edward J.Anthony Paul S.Fennell 《Frontiers of Environmental Science & Engineering》 SCIE EI CSCD 2022年第7期113-124,共12页
Is it possible to improve CO_(2)solubility in potassium carbonate(K_(2)CO_(3))-based transition temperature mixtures(TTMs)?To assess this possibility,a ternary transition-temperature mixture(TTTM)was prepared by using... Is it possible to improve CO_(2)solubility in potassium carbonate(K_(2)CO_(3))-based transition temperature mixtures(TTMs)?To assess this possibility,a ternary transition-temperature mixture(TTTM)was prepared by using a hindered amine,2-amino-2-methyl-1,3-propanediol(AMPD).Fourier transform infrared spectroscopy(FT-IR)was employed to detect the functional groups including hydroxyl,amine,carbonate ion,and aliphatic functional groups in the prepared solvents.From thermogravimetric analysis(TGA),it was found that the addition of AMPD to the binary mixture can increase the thermal stability of TTTM.The viscosity findings showed that TTTM has a higher viscosity than TTM while their difference was decreased by increasing temperature.In addition,Eyring’s absolute rate theory was used to compute the activation parameters(∆G^(*),∆H^(*),and ∆S^(*)).The CO_(2)solubility in liquids was measured at a temperature of 303.15 K and pressures up to 1.8 MPa.The results disclosed that the CO_(2)solubility of TTTM was improved by the addition of AMPD.At the pressure of about 1.8 MPa,the CO_(2)mole fractions of TTM and TTTM were 0.1697 and 0.2022,respectively.To confirm the experimental data,density functional theory(DFT)was employed.From the DFT analysis,it was found that the TTTM+CO_(2)system has higher interaction energy(|∆E|)than the TTM+CO_(2)system indicating the higher CO_(2)affinity of the former system.This study might help scientists to better understand and to improve CO_(2)solubility in these types of solvents by choosing a suitable amine as HBD and finding the best combination of HBA and HBD. 展开更多
关键词 Ternary transition-temperature mixture FT-IR and thermal stability analysis Viscosity and correlation study Eyring’s absolute rate theory CO_(2)solubility Density functional theory(DFT)
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