Liu Jinn-Liang, Eisenberg Bob
Institute of Computational and Modeling Science, National Tsing Hua University, Hsinchu 300, Taiwan.
Department of Physiology and Biophysics, Rush University, Chicago, IL 60612, USA.
Entropy (Basel). 2020 May 14;22(5):550. doi: 10.3390/e22050550.
We have developed a molecular mean-field theory-fourth-order Poisson-Nernst-Planck-Bikerman theory-for modeling ionic and water flows in biological ion channels by treating ions and water molecules of any volume and shape with interstitial voids, polarization of water, and ion-ion and ion-water correlations. The theory can also be used to study thermodynamic and electrokinetic properties of electrolyte solutions in batteries, fuel cells, nanopores, porous media including cement, geothermal brines, the oceanic system, etc. The theory can compute electric and steric energies from all atoms in a protein and all ions and water molecules in a channel pore while keeping electrolyte solutions in the extra- and intracellular baths as a continuum dielectric medium with complex properties that mimic experimental data. The theory has been verified with experiments and molecular dynamics data from the gramicidin A channel, L-type calcium channel, potassium channel, and sodium/calcium exchanger with real structures from the Protein Data Bank. It was also verified with the experimental or Monte Carlo data of electric double-layer differential capacitance and ion activities in aqueous electrolyte solutions. We give an in-depth review of the literature about the most novel properties of the theory, namely Fermi distributions of water and ions as classical particles with excluded volumes and dynamic correlations that depend on salt concentration, composition, temperature, pressure, far-field boundary conditions etc. in a complex and complicated way as reported in a wide range of experiments. The dynamic correlations are self-consistent output functions from a fourth-order differential operator that describes ion-ion and ion-water correlations, the dielectric response (permittivity) of ionic solutions, and the polarization of water molecules with a single correlation length parameter.
我们已经开发出一种分子平均场理论——四阶泊松-能斯特-普朗克-比克曼理论——用于通过处理具有间隙空隙、水的极化以及离子-离子和离子-水相关性的任意体积和形状的离子与水分子,来对生物离子通道中的离子和水流进行建模。该理论还可用于研究电池、燃料电池、纳米孔、包括水泥在内的多孔介质、地热盐水、海洋系统等中的电解质溶液的热力学和电动性质。该理论能够计算蛋白质中所有原子以及通道孔中所有离子和水分子的电能量和空间能量,同时将细胞外和细胞内浴中的电解质溶液视为具有模拟实验数据的复杂性质的连续介质。该理论已通过来自短杆菌肽A通道、L型钙通道、钾通道以及具有蛋白质数据库真实结构的钠/钙交换器的实验和分子动力学数据得到验证。它还通过电解质水溶液中双电层微分电容和离子活度的实验或蒙特卡罗数据得到验证。我们对有关该理论最新颖性质的文献进行了深入综述,即水和离子作为具有排除体积的经典粒子的费米分布以及动态相关性,这些相关性以复杂的方式取决于盐浓度、组成、温度、压力、远场边界条件等,正如在广泛的实验中所报道的那样。动态相关性是一个四阶微分算子的自洽输出函数,该算子描述离子-离子和离子-水相关性、离子溶液的介电响应(电容率)以及具有单个相关长度参数的水分子极化。