基于AMOEBA可极化力场研究蛋白二聚化对于gramicidin A通道电导的影响（英文）

在离子通道性质的研究中,由于可极化力场计算量巨大,长期以来使用最广泛的依旧是经典力场.本文考察了可极化力场在描述离子通道gramicidin A(gA)二聚状态下离子输运性质方面的可靠性.利用AMOEBA可极化力场对单通道gA和双通道gA进行增强采样模拟,从电导、扩散系数和自由能等方面描述了gA二聚化对钾离子和钠离子穿越通道过程的影响.计算结果显示,可极化力场模拟获得的钾离子和钠离子穿越通道的电导与实验数值吻合.进一步的数据分析揭示了蛋白质二聚化影响gA通道离子输运性质的分子机制,即蛋白二聚化通过调整gA蛋白周围的环境(磷脂头基、通道外离子和体相水分子的分布)而不是直接调整gA蛋白的构象来加速钾离子和钠离子穿越通道.     

离子通道的非均匀分布对环链神经元网络电活动的影响

在电位耦合条件下,利用Morris-Lecar神经元模型构造环链神经元网络,研究了离子通道分布不均匀情形下神经元网络群体电活动的演化和转变问题. 在数值研究中通过改变局部区域的离子通道电导值模拟离子通道的非均匀分布,并对其可能的机制进行了分析. 还研究了网络中局部区域的钙离子电导的差异性和钾离子电导的差异性如何逐渐激发周边神经元,以及诱发的行波如何依赖于神经元之间的耦合强度. 研究发现,增大钙离子电导到一定程度或减小钾离子电导到一定程度可以诱发周围神经元产生兴奋并产生稳定的行波;相反,减小钙离子电导或增大钾离子电导则会减缓或阻断行波的传递. 在同时改变钙离子电导和钾离子电导的情况下,行波的诱发和传播完全依赖于钙离子电导的增量和钾离子电导的减量. 关键词： Morris-Lecar神经元 离子通道的非均匀分布 环链网络     

基于参考势的从头算量子力学/分子力学混合方法研究Parvalbumin B蛋白结合钙、镁离子的选择性

蛋白的离子选择性与蛋白的功能密切相关,而离子选择性本质上来源于蛋白分子与离子结合自由能的差别. 尽管近几十年来分子力场在描述蛋白体系相互作用方面取得了长足的进步,由于缺乏对静电极化和电荷转移效应显式的描述,传统的分子力场依然难以精确地描述金属蛋白体系中蛋白质与金属离子的相互作用. 量子化学方法非常适合于蛋白质与金属离子之间相互作用的描述. 但是在分子模拟中采用量子化学方法则太昂贵了. 近年来发展起来的参考势方法在保证计算精度的前提下兼顾效率,可以有效地解决这个窘境. 在这个方法中,动力学模拟的轨迹是在分子力场的精度下获得的. 随后,通过从分子力场到量子化学方法的矫正,从而获得在量子化学势函数级别下的自由能信息. 本文采用参考势函数方法研究了Parvalbumin B蛋白的结合口袋对钙、镁离子的选择性. 计算结果表明电荷转移效应非常重要,而量子化学方法可以比较精确地预测离子的选择性. 并且,量子化学区域的选择对于结果的可靠性也是非常重要的.     

基于参考势的从头算量子力学/分子力学混合方法研究Parvalbumin B蛋白结合钙、镁离子的选择性（英文）

蛋白的离子选择性与蛋白的功能密切相关,而离子选择性本质上来源于蛋白分子与离子结合自由能的差别.尽管近几十年来分子力场在描述蛋白体系相互作用方面取得了长足的进步,由于缺乏对静电极化和电荷转移效应显式的描述,传统的分子力场依然难以精确地描述金属蛋白体系中蛋白质与金属离子的相互作用.量子化学方法非常适合于蛋白质与金属离子之间相互作用的描述.但是在分子模拟中采用量子化学方法则太昂贵了.近年来发展起来的参考势方法在保证计算精度的前提下兼顾效率,可以有效地解决这个窘境.在这个方法中,动力学模拟的轨迹是在分子力场的精度下获得的.随后,通过从分子力场到量子化学方法的矫正,从而获得在量子化学势函数级别下的自由能信息.本文采用参考势函数方法研究了Parvalbumin B蛋白的结合口袋对钙、镁离子的选择性.计算结果表明电荷转移效应非常重要,而量子化学方法可以比较精确地预测离子的选择性.并且,量子化学区域的选择对于结果的可靠性也是非常重要的.     

极化蛋白专一性电荷在HIV-1蛋白酶-抑制剂结合自由能预测中的应用

对人类免疫缺陷病毒（HIV-1）蛋白酶-抑制剂复合物分别在AMBER力场及极化专一性蛋白电荷（PPC）下进行10 ns的分子动力学模拟（MD）,并用MM/PBSA方法计算结合自由能.PPC是基于线性标度的量子力学计算的静电势拟合的蛋白质电荷,能够更准确地描述蛋白质所处的静电环境.结果表明：PPC电荷计算的结合自由能比AMBER力场计算的结合自由能更接近实验值.     

随机中毒对神经元网络时空动力学行为的影响

神经元细胞膜上的离子通道能够被一些有毒的化学物质阻断. 离子通道阻断会降低离子通道的电导率和激活通道数, 影响神经元的放电活动, 进而影响神经网络时空模式的动力学行为. 本文采用具有周期边界的近邻耦合Hodgkin-Huxley神经元网络, 数值研究了钠离子和钾离子通道随机中毒时神经网络时空模式的演化过程. 发现钠离子和钾离子通道随机中毒可以导致螺旋波破裂. 通过分析网络的放电概率, 发现钠离子通道随机中毒降低了神经网络的兴奋性, 且其对中毒的敏感程度与噪声强度有关; 钾离子通道随机中毒增强了神经网络的兴奋性. 与均匀的通道中毒相比, 随机通道中毒的神经网络具有更丰富的动力学行为. 最后, 采用无流边界条件对神经网络进行数值仿真, 得到了类似的结果. 该研究更真实地反映神经系统中毒时整体兴奋性的变化, 从另一个方面揭示离子通道中毒对网络时空行为的影响, 有利于更进一步理解离子通道在网络整体行为中的作用. 关键词： 神经网络 离子通道 随机中毒 时空动力学     

苯基分子器件量子相干输运第一性原理研究

分子器件在纳米尺度下,电子的相干性将对体系的电导产生重大影响.本文基于第一性原理计算研究了苯分子连接于一维金属电极下的电荷输运性质.发现一维金电极连接下,不同的连接方式(para与meta)体系下的电导将会有显著差别,而一维铂电极连接下,体系的电导差别不大.我们通过计算电极的能带,发现金电极与铂电极在费米面处的散射态数目有差别.当量子相干效应导致散射态局域化发生改变时,由于铂电极的通道数较多,电子依然可以通过扩展的通道输运,因此不同连接方式下的电导变化不明显.     

离子与通道相互作用对NaK 通道通透特性影响的研究

以NaK 通道的三维精细结构为基础,从理论上阐述了NaK 通道对钠离子、钾离子、铷离子以及钙离子的通透机理,钡离子可以作为NaK 通道阻断剂的微观机理,我们的研究结果表明,通道与离子的相互作用是决定通道对不同离子选择性的基础, 反映通道与离子相互作用的位能曲线是通道对不同离子通透性的外在表现. 关键词： NaK 通道 密度泛函 布朗动力学 通透性     

含stubs量子波导系统的电子自旋极化输运性质

理论上研究了含stubs的Rashba自旋轨道耦合（spin-orbit coupling, SOC）量子波导系统的自旋极化输运性质. 利用晶格格林函数方法,发现由于stubs和SOC产生的势阱使系统中出现束缚态,这些束缚态与传播态之间相互干涉导致电导中出现Fano共振结构,同时在对应的自旋极化率中也出现Fano共振或反共振结构. 此外,由于系统结构的突变使电子被反向散射和量子干涉效应,电导中出现一系列的共振峰. 但是,当系统加上外磁场后,所有这些效应都被抑制, 系统重新出现量子化电导, 同时自旋电导也出 关键词： 量子波导 自旋极化输运 自旋轨道耦合     

通过嵌入铁磁电极之间 Aharonov-Bohm 干涉仪自旋极化输运性质的研究

使用非平衡态格林函数方法和运动方程近似,研究了嵌入铁磁电极之间Aharonov-Bohm 干涉仪的自旋极化输运性质.在左右铁磁电极平行和反平行两种磁组态下,结合Fano因子分析和讨论了Fano 和Kondo 共振对该系统电导的影响,以及电导随自旋极化强度和磁通的变化.结果表明,自旋极化强度和磁通能有效地调节和控制电导,但电导的线形主要由磁通决定;在适当的条件下能导致大的正磁阻和负磁阻的出现.因此,该系统是一个很好的自旋阀晶体管,在自旋电子学中有潜在的应用价值. 关键词： Fano和Kondo共振 自旋极化强度 Fano因子 隧道磁阻     

Molecular dynamics study on the field effect ion transport in carbon nanotube

We investigated potassium ion transport in the (5, 5) carbon nanotube by using classical molecular dynamics simulations under applying external force fields. This can be applied to nanoscale ionic-field-effect devices. As the applying external force field increases, the potassium ions rapidly go through the nanochannel. Under the low external force fields, the thermal fluctuation of the nanochannel affected on the tunneling of the potassium ions, whereas the effects of the thermal fluctuation were negligible under the high external force fields.     

Specific ion adsorption at hydrophobic solid surfaces

Molecular dynamics simulations of ions at a hydrophobic self-assembled monolayer with polarizable force fields for water and ions are used to extract potentials of mean force for Na+ and the halide ions Cl-, Br-, and I-. Similar to the air-water interface, the large halide ions are attracted to the surface, which is traced back to surface-modified ion hydration. The total effective interaction is parametrized and used within Poisson-Boltzmann theory to calculate surface potentials and interfacial tensions at finite ion concentration in qualitative agreement with experiments.     

Molecular dynamics simulation of continuous current flow through a model biological membrane channel

The conductance of sodium ions through a simplified channel-membrane system immersed in a reservoir of 1M NaCl in SPC/E water is examined by molecular dynamics simulation. An applied external potential of 1.1 V drives the ions and water through a channel of length 25 A producing a current of 19.6 pA, in reasonable agreement with experimental findings. The stream of ions and water molecules flows continuously because of the constant applied field and periodic boundary conditions. We also examine the potential profile across the simulation cell, the average density distributions of the various species in the reservoir and radially in the channel, and the ion velocity in the channel.     

Robustness,Death of Spiral Wave in the Network of Neurons under Partial Ion Channel Block

The development of spiral wave in a two-dimensional square array due to partial ion channel block (Potas- sium, Sodium) is investigated, the dynamics of the node is described by Hodgkin-Huxley neuron and these neurons are coupled with nearest neighbor connection. The parameter ratio x Na (and xK ), which defines the ratio of working ion channel number of sodium (potassium) to the total ion channel number of sodium (and potassium), is used to measure the shift conductance induced by channel block. The distribution of statistical variable R in the two-parameter phase space (parameter ratio vs. poisoning area) is extensively calculated to mark the parameter region for transition of spiral wave induced by partial ion channel block, the area with smaller factors of synchronization R is associated the parameter region that spiral wave keeps alive and robust to the channel poisoning. Spiral wave keeps alive when the poisoned area (potassium or sodium) and degree of intoxication are small, distinct transition (death, several spiral waves coexist or multi-arm spiral wave emergence) occurs under moderate ratio x Na (and xK ) when the size of blocked area exceeds certain thresholds. Breakup of spiral wave occurs and multi-arm of spiral waves are observed when the channel noise is considered.     

Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications.     

Na<Superscript>+</Superscript>/K<Superscript>+</Superscript> selectivity in the formation of ion pairs in aqueous solutions

The integral equations of liquids (RISM) and molecular dynamics method were used to calculate the mean force potential for the SO₃ and COO hydrophilic groups and the CH₃ hydrophobic group in the acetate, methyl sulfonate, and hydrosulfate anions, which form ion pairs with sodium and potassium cations in water. The carboxyl group selectively binds sodium ions from solutions containing Na⁺ and K⁺ ions, in spite of their equal charges, because the potassium ion experiences stronger steric hindrances near this group compared with sodium. The biophysical consequences of the revealed selectivity are discussed.     

形变碳纳米管选择通过性的分子动力学研究

本文采用分子动力学方法, 研究了基团修饰后形变碳纳米管的水分子通过性和离子选择性. 结果表明, 形变碳纳米管的短径与修饰基团的种类、修饰率及修饰位置有关. 不同粗细碳纳米管均存在临界短径, 小于临界短径的形变碳纳米管具有对氯离子和钠离子的选择性, 同时水分子通过速率与本征碳纳米管相比未明显变小. 分析系统平均力势表明, 离子选择性来源于不同短径碳纳米管管口的通过势垒. 对于实际制备中较宽孔径分布的碳纳米管, 可以通过基团修饰等方法调控其短径, 提高其离子选择性.     

Effects of channel noise on firing coherence of small-world Hodgkin-Huxley neuronal networks

We investigate the effects of channel noise on firing coherence of Watts-Strogatz small-world networks consisting of biophysically realistic HH neurons having a fraction of blocked voltage-gated sodium and potassium ion channels embedded in their neuronal membranes. The intensity of channel noise is determined by the number of non-blocked ion channels, which depends on the fraction of working ion channels and the membrane patch size with the assumption of homogeneous ion channel density. We find that firing coherence of the neuronal network can be either enhanced or reduced depending on the source of channel noise. As shown in this paper, sodium channel noise reduces firing coherence of neuronal networks; in contrast, potassium channel noise enhances it. Furthermore, compared with potassium channel noise, sodium channel noise plays a dominant role in affecting firing coherence of the neuronal network. Moreover, we declare that the observed phenomena are independent of the rewiring probability.     

Precision laser spectroscopy of highly charged ions

Recently, intense beams of highly charged ions have become available at heavy ion cooler rings. The obstacle for producing these highly interesting candidates is the large binding energy of K-shell electrons in heavy systems in excess of 100 keV. One way to remove these electrons is to strip them off by passing the ion through material. In the cooler ring, the ions are cooled to a well defined velocity. At the SIS/ESR complex it is possible to produce, store, and cool highly charged ions up to bare uranium with intensities exceeding 10⁸ atoms in the ring. This opens the door for precision laser spectroscopy of hydrogenlike-heavy ions, e.g.²⁰⁹Bi⁸²⁺, and allows to examine the interaction of the single electron with the large fields of the heavy nucleus, exceeding any artificially produced electric and magnetic fields by orders of magnitude. In the electron cooler the interaction of electrons and highly charged ions otherwise only present in the hottest plasmas can be studied.