共查询到20条相似文献,搜索用时 15 毫秒
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提出一种计算热导率的非平衡分子动力学(NEMD)方法,通过构造均匀内热源获得抛物线形温度分布,并基于Fourier导热定律计算热导率,与Müller-Plathe发展的反扰动非平衡分子动力学(RNEMD)方法相比,不仅具有能量动量守恒和收敛性好的优点,还克服了常规NEMD方法中热冷源区域存在局域热力学非平衡的问题,并有模拟系统温差影响小的特点.对液态氩的热导率进行模拟并与RNEMD方法的模拟结果进行对比. 相似文献
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瞬态涡旋动力学与非平衡体系中的异常核现象 总被引:1,自引:0,他引:1
根据实验现象和已发表的数据,对电解过程中的尖端效应、磁自收缩现象、阴极表面电化学双层的高能集中、极化核聚变的产生进行了分析研究.利用CR 39固体径迹探测器记录到电化学系统中高度集中而且准直的10MeV以上的异常高能带电粒子.提出了涡旋动力学理论解释电化学放电过程中的异常现象———过剩热和非平衡系统中的异常核现象. The tip effect, magnetism self-pinch phenomena, high energy concentration on the cathode surface, electrochemical double layer, and polarized nucleus fusion in the process of electrolysis have been studied and discussed. The high concentrated and straight charged particles with energy above 10 MeV in (electrochemistry) systems were recorded by CR-39 solid trace detector. The hypothesis of vortex dynamics is proposed for explaining the peculiarities of excess heat and anomalous nucleus phenomena... 相似文献
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p53-MDM2相互作用的抑制已经成为治疗癌症的新方法. 本文将分子动力学模拟和MM-PBSA(molecular mechanics/passion-Boltzman surface area)方法结合起来研究MDM2-p53相互作用机制. 结果证明范德华相互作用驱动了MDM2与p53的结合. 基于残基-残基相互作用的计算不仅证明p53的三个残基Phe19′, Trp23′和Leu26′与MDM2有较强的相互作用,而且还发现另外两个残基Leu22′和Pro27′也与MDM2有较强的相互作用,这为抗癌药物的设计提供了新靶标. 同时也证明CH-CH,CH-π和π-π相互作用驱动了p53在MDM2疏水性裂缝中的结合. 相似文献
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Dynamics analysis of chaotic maps: From perspective on parameter estimation by meta-heuristic algorithm 下载免费PDF全文
Chaotic encryption is one of hot topics in cryptography, which has received increasing attention. Among many encryption methods, chaotic map is employed as an important source of pseudo-random numbers(PRNS). Although the randomness and the butterfly effect of chaotic map make the generated sequence look very confused, its essence is still the deterministic behavior generated by a set of deterministic parameters. Therefore, the unceasing improved parameter estimation technology becomes one of potential threats for chaotic encryption, enhancing the attacking effect of the deciphering methods. In this paper, for better analyzing the cryptography, we focus on investigating the condition of chaotic maps to resist parameter estimation. An improved particle swarm optimization(IPSO) algorithm is introduced as the estimation method. Furthermore, a new piecewise principle is proposed for increasing estimation precision. Detailed experimental results demonstrate the effectiveness of the new estimation principle, and some new requirements are summarized for a secure chaotic encryption system. 相似文献
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Carsten Hartmann 《Journal of statistical physics》2008,130(4):687-711
This article addresses the problem of computing the Gibbs distribution of a Hamiltonian system that is subject to holonomic
constraints. In doing so, we extend recent ideas of Cancès et al. (M2AN 41(2), 351–389, 2007) who could prove a Law of Large Numbers for unconstrained molecular systems with a separable Hamiltonian employing a discrete
version of Hamilton’s principle. Studying ergodicity for constrained Hamiltonian systems, we specifically focus on the numerical
discretization error: even if the continuous system is perfectly ergodic this property is typically not preserved by the numerical
discretization. The discretization error is taken care of by means of a hybrid Monte-Carlo algorithm that allows for sampling
bias-free expectation values with respect to the Gibbs measure independently of the (stable) step-size. We give a demonstration
of the sampling algorithm by calculating the free energy profile of a small peptide. 相似文献
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利用自由能方法的分子动力学模拟,计算了零压下Al的熔化温度.在计算液相自由能的过程中,采用勒纳-琼斯(LJ)液体作为参考系统,同时将计算结果与Mei和Davenport等人的计算结果进行了比较,计算结果表明:1)选用LJ参考系统使液相自由能的计算时间节省一半,并且不影响熔化温度的计算结果;2)采用不同的埋入原子势(EAM)的分子动力学模拟计算得到的熔化温度与实验值都存在偏差,而就金属Al而言,采用Cai等人的EAM势的熔化温度的计算结果比Mei和Davenport及Morris等人采用的势模型的结果略有改
关键词:
熔化温度
自由能方法
分子动力学模拟 相似文献
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王青 《原子与分子物理学报》2017,34(6)
氢键和极性相互作用在抑制剂-蛋白结合专一性识别过程中起到重要作用. 抑制剂Benzamidine(BEN)与胰岛素trypsin相互作用机制的阐明有助于胰岛素高效抑制剂的研发.本文采用分子动力学模拟和MM-PBSA(molecular mechanics-Poisson Boltzmann surface area)从原子层次上研究BEN与胰岛素的结合模式.结果表明抑制剂BEN的脒基不仅与Asp189的羰基产生静电相互作用,而且与残基Ser190和Gly214形成氢键相互作用.基于残基能量分解的计算表明抑制剂的苯基与残基His58, Cys191, Gln192, Trp211, Gly212和Cys215形成有利于抑制剂结合的疏水性相互作用.期望当前的研究能为胰岛素有效抑制剂的研发提供重要的理论指导. 相似文献
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微小液滴在不同能量表面上的润湿状态对于准确预测非均相核化速率和揭示界面效应影响液滴增长微观机理具有重要意义. 通过分子动力学模拟, 研究了纳米级液滴在不同能量表面上的铺展过程和润湿形态. 结果表明, 固液界面自由能随固液作用强度增加而增加, 并呈现不同液滴铺展速率和润湿特性. 固液作用强度小于1.6的低能表面呈现疏水特征, 继续增强固液作用强度时表面变为亲水, 而固液作用强度大于3.5的高能表面上液体呈完全润湿特征. 受微尺度条件下非连续、非对称作用力影响, 微液滴气液界面存在明显波动, 呈现与宏观液滴不同的界面特征. 统计意义下, 微小液滴在不同能量表面上铺展后仍可以形成特定接触角, 该接触角随固液作用强度增加而线性减小, 模拟结果与经典润湿理论计算获得的结果呈现相似变化趋势. 模拟结果从分子尺度为核化理论中的毛细假设提供了理论支持, 揭示了液滴气液界面和接触角的波动现象, 为核化速率理论预测结果和实验测定结果之间的差异提供了定性解释. 相似文献
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氢键和极性相互作用在抑制剂-蛋白结合专一性识别过程中起到重要作用.抑制剂Benzamidine(BEN)与胰岛素trypsin相互作用机制的阐明有助于胰岛素高效抑制剂的研发.本文采用分子动力学模拟和MM-PBSA(molecular mechanics-Poisson Boltzmann surface area)从原子层次上研究BEN与胰岛素的结合模式.结果表明抑制剂BEN的脒基不仅与Asp189的羰基产生静电相互作用,而且与残基Ser190和Gly214形成氢键相互作用.基于残基能量分解的计算表明抑制剂的苯基与残基His58,Cys191,Gln192,Trp211,Gly212和Cys215形成有利于抑制剂结合的疏水性相互作用.期望当前的研究能为胰岛素有效抑制剂的研发提供重要的理论指导. 相似文献
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在李代数动力学群得到Hamiltonian的基础上,通过求解正则运动方程.对固定键角近似下臭氧分子体系相空间的庞加莱截面、KAM环面以及振动体系的能量属性进行了研究,获得了有关臭氧分子振动体系丰富的动力学信息. 相似文献
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Asp25质子化有利于HIV-1蛋白酶与抑制剂GRL02031结合 总被引:1,自引:1,他引:0
GRL02031是人体免疫缺陷病毒(HIV-1)天冬氨酸蛋白酶的抑制剂,是潜在的治疗艾滋病药物,HIV-1蛋白酶中Asp25/Asp25'的质子化状态对于理解HIV-1 蛋白酶和抑制剂的作用机制以及氨基酸变异对抗药性的影响有重要意义。本文对Protease-GRL02031(PR-031)复合物的最可能的四种质子化状态进行了5ns分子动力学模拟,分析了Asp25/Asp25'不同的质子化状态对动力学特征和作用机制的影响,用MM-PBSA的方法计算了PR-031复合物在各种质子化状态下的结合自由能,同时对作为PR-031作用桥梁的水分子与PR-031复合物形成氢键的分析,表明水分子在ASP25质子化状态下最为稳定。结果显示A链ASP25中OD2质子化更有利于蛋白酶与抑制剂GRL- 02031的结合,是最可能的质子化状态。这对更高效的抗变异药物的设计提供了理论上的指导。 相似文献
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《Molecular physics》2012,110(11-12):1081-1095
We compare the Free Energy Perturbation (FEP) and Thermodynamic Integration (TI) approaches in slab-geometries where the electrostatic interactions are handled with the standard three-dimensionally Ewald summation technique. The comparison between FEP and TI is made through energy distributions in the analysis of the phase space sampling between the forward and backward directions, the reversibility of the perturbation, the number of windows and the consistency of the free energy decomposition into individual components. We report here free energy calculations in order to predict the shift in the redox potential in self-assembled monolayers (SAMs) as the coadsorbed chain length is changed. The reproduction of the free energies with respect to the electrolyte is tested on neutral and charged simulation cells. 相似文献
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Yuki Mitsuta Johannes Kästner Shusuke Yamanaka Takashi Kawakami Mitsutaka Okumura 《Molecular physics》2019,117(17):2284-2292
ABSTRACTWe have investigated the free energy surface of alanine tripeptide in water. To elucidate the secondary structure of the amide chain, information on the free energy surface with explicit water at room temperature, and the multidimensional reaction coordinates are required. We studied the minimum free energy paths (MFEPs) connecting reactants, transition structures (TS) and products. To solve this problem, we used the free energy reaction root mapping (FERRMap) method. This is an automated search method to find MFEPs by using umbrella integration and the scaled hypersphere search method. We calculated the four-dimensional free energy surface for alanine tripeptide in water using FERRMap and found 61 equilibrium structures (EQ) connected by 133 TS points. After elucidating the MFEP network, we analysed the structures of the EQ points and the MFEPs connecting beta-sheet structures and beta-turn structures or left-handed helix structures. 相似文献
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针对分子动力学模拟中碳纳米管的结构优化问题,提出了一种新的优化算法.新的优化算法在遗传算法的基础上,引入了克隆选择机理和模拟退火技术.对五个典型函数的优化测试结果表明,该算法搜索过程稳定性好,可较好地实现全局最优.将其应用于碳纳米管原子结构优化,加快了能量优化速度,提高了优化质量.模拟结果说明,混合遗传算法的优化时间随原子数增加而呈线性增长.在碳纳米管原子数较多时,结构优化时间比共轭梯度法降低一个数量级左右,大大降低了系统的模拟时间.
关键词:
分子动力学
碳纳米管
能量优化
遗传算法
克隆选择算法 相似文献