Concentration polarization in translocation of DNA through nanopores and nanochannels

In this Letter we provide a theory to show that high-field electrokinetic translocation of DNA through nanopores or nanochannels causes large transient variations of the ionic concentrations in front and at the back of the DNA due to concentration polarization (CP). The CP causes strong local conductivity variations, which can successfully explain the nontrivial current transients and ionic distributions observed in molecular dynamics simulations of nanopore DNA translocations as well as the transient current dips and spikes measured for translocating hairpin DNA. Most importantly, as the future of sequencing of DNA by nanopore translocation will be based on time-varying electrical conductance, CP, must be considered in experimental design and interpretation--currently these studies are mostly based on the incomplete pore conductance models that ignore CP and transients in the electrical conductance.     

Probing nanotube-nanopore interactions

We demonstrate a new nanoscale system consisting of a nanotube threaded through a nanopore in aqueous solution. Its electrical and mechanical properties are sensitive to experimentally controllable conformational changes on sub-Angstrom length scales. Ionic current transport through a nanopore is significantly suppressed by the threading nanotube and the mechanical interactions between the nanotube and pore are accounted for by a folding geometry. The experiments provide first measurements of the longitudinal resolution and metrology of a solid-state nanopore "microscope." This new nanostructure provides a means to study molecule-nanotube interactions in conducting ionic solutions as well as geometrical and surface properties of nanopores and nanotubes.     

Ionic capillary evaporation in weakly charged nanopores

Using a variational field theory, we show that an electrolyte confined to a neutral cylindrical nanopore traversing a low dielectric membrane exhibits a first-order ionic liquid-vapor pseudo-phase-transition from an ionic-penetration "liquid" phase to an ionic-exclusion "vapor" phase, controlled by nanopore-modified ionic correlations and dielectric repulsion. For weakly charged nanopores, this pseudotransition survives and may shed light on the mechanism behind the rapid switching of nanopore conductivity observed in experiments.     

Highly Efficient Power Conversion from Salinity Gradients with Ion-Selective Polymeric Nanopores

A polymeric nanopore membrane with selective ionic transport has been proposed as a potential device to convert the chemical potential energy in salinity gradients to electrical power.However,its energy conversion efficiency and power density are often limited due to the challenge in reliably controlling the size of the nanopores with the conventional chemical etching method.Here we report that without chemical etching,polyimide(PI) membranes irradiated with GeV heavy ions have negatively charged nanopores,showing nearly perfect selectivity for cations over anions,and they can generate electrical power from salinity gradients.We further demonstrate that the power generation efficiency of the PI membrane approaches the theoretical limit,and the maximum power density reaches 130mW/m2 with a modified etching method,outperforming the previous energy conversion device that was made of polymeric nanopore membranes.     

Pink noise of ionic conductance through single artificial nanopores revisited

We report voltage-clamp measurements through single conical nanopore obtained by chemical etching of a single ion track in polyimide film. Special attention is paid to the pink noise of the ionic current (i.e., 1/f noise) measured with different filling liquids. The relative pink-noise amplitude is almost independent of concentration and pH for KCl solutions, but varies strongly using ionic liquids. In particular, we show that depending on the ionic liquid, the transport of charge carriers is strongly facilitated (low noise and higher conductivity than in the bulk) or jammed. These results show that the origin of the pink noise can be ascribed neither to fluctuations of the pore geometry nor to the pore wall charges, but rather to a cooperative effect on ions motion in confined geometry.     

利用纳米孔研究DNA

脱氧核糖核酸 (DNA)和蛋白质是构成生命体最为重要的两类生物大分子 .随着科学技术的快速发展 ,越来越多的纳米技术被用来研究这些生物大分子 .文章详细介绍了近来利用纳米孔技术研究DNA的一些进展 .结合作者近期利用聚焦离子束 (FIB)制作纳米孔的工作 ,提出了利用纳米孔解离核小体的设想 .如果能够利用纳米孔将双螺旋DNA从组蛋白八聚体上剥离下来 ,并探测这一过程 ,将揭示核小体中包含的许多生物化学、物理信息 .文章对此进行了较为详细的分析 :处于电场中的核小体在电场的作用下 ,DNA分子穿越纳米孔 ,同时由于纳米孔的阻挡力 ,使组蛋白不能穿越 ,从而诱使DNA从组蛋白八聚体上分离下来 .通过准确检测DNA分子穿孔过程中引起的电流阻塞效应 ,可将DNA与组蛋白的相互作用的一些性质反映出来     

Controlling ionic current through a nanopore by tuning pH: a local equilibrium Monte Carlo study

ABSTRACT

The purpose of this work is to create a model of a nanofluidic transistor which is able to mimic the effects of pH on nanopore conductance. The pH of the electrolyte is an experimentally controllable parameter through which the charge pattern can be tuned: pH affects the ratio of the protonated/deprotonated forms of the functional groups anchored to the surface of the nanopore (for example, amino and carboxyl groups). Thus, the behaviour of the bipolar transistor changes as it becomes ion selective in acidic/basic environments. We relate the surface charge to pH and perform particle simulations (Local Equilibrium Monte Carlo) with different nanopore geometries (cylindrical and double conical). The simulations form a self consistent system with the Nernst–Planck equation with which we compute ionic flux. We discuss the mechanism behind pH-control of ionic current: formation of depletion zones.     

Counterion-hopping along the backbone of single-stranded DNA in nanometer pores: a mechanism for current conduction

Molecular dynamics calculations are performed to investigate ionic current conduction through nanopores in the presence of single-stranded DNA. We find the counterions to be strongly attracted to the phosphate groups of the DNA, with resident time on the order of nanoseconds, while coions are strongly excluded. The diffusion constant of the counterions is calculated and used to estimate the ionic current through the pore, which gives a similar magnitude as in experiment. The results suggest a counterion-hopping mechanism along the ssDNA backbone in the current conduction through nanopores.     

离子浓度及表面结构对岩石孔隙内水流动特性的影响

酸性环境引发的岩石孔隙表面溶解增加了孔隙内水溶液的盐离子浓度,破坏了孔隙的表面结构.本文采用分子动力学模拟的方法研究了纳米级岩石孔隙内水溶液的流动特性,分析了盐离子浓度和孔隙表面结构对水流速度分布的影响及原因.研究结果表明:纳米级岩石孔隙内的水溶液流动符合泊肃叶流动特性,流速呈"抛物线"分布;随盐离子浓度增加,水溶液内部氢键网络变得更为致密,水黏度随其呈线性增长;水溶液中离子浓度越大,孔隙表面对水流动的阻力越大,最大流速越小,速度分布的"抛物线"曲率半径越大;岩石孔隙表面结构的破坏改变了流动表面的粗糙程度,增加了孔隙表面对H2O分子的吸引力.随表面结构破坏程度的增大,水溶液在近壁区域的密度增大,流速降低;当表面破坏程度达到50%时,水溶液在近壁区域出现了明显的负边界滑移现象.     

Water Transport through Multinanopores Membranes

We investigate the influence of correlation between water molecules transport through the neighbouring nanopores, whose centres are at a distance of only 6.2A, using the molecular dynamics simulations. Water molecule distribution in nanopore and average water flow are obtained. It is found that the average water molecule number and water flow are slightly different between a system made of the neighbouring nanopores and a system of a single pore. This indicates that transport of water chains in neighbouring pores do no show significant influence each other. These findings should be helpful in designing efficient artificial membrane made of nanopores and providing an insight into effects of the biological channel structure on the water permeation.     

Effect of salt concentration on the electrophoretic speed of a polyelectrolyte through a nanopore

In a previous paper [S. Ghosal, Phys. Rev. E 74, 041901 (2006)] a hydrodynamic model for determining the electrophoretic speed of a polyelectrolyte through an axially symmetric slowly varying nanopore was presented in the limit of a vanishingly small Debye length. Here the case of a finite Debye layer thickness is considered while restricting the pore geometry to that of a cylinder of length much larger than the diameter. Further, the possibility of a uniform surface charge on the walls of the nanopore is taken into account. It is thereby shown that the calculated transit times are consistent with recent measurements in silicon nanopores.     

Water wettability in nanoconfined environment

Water confined in nanoscale space behaves quite differently from that in the bulk.For example,in biological aquaporins and in carbon nanotubes,the traversing water molecules form a single file configuration.Water would stay in vapor state in extremely hydrophobic narrow nanopores owing to the physicochemical interactions between the water molecules and the surface of the nanopore.A spontaneous wet-dry transition has been identified in both biological and artificial nanopores.The nanopore is either fulfilled with liquid water or completely empty.Based on this mechanism,the wetting and dewetting processes inside nanopores have been further developed into highly efficient nanofluidic gates that can be switched by external stimuli,such as light irradiation,electric potential,temperature,and mechanical pressure.This review briefly covers the recent progress in the special wettability in nanoconfined environment,water transportation through biological or artificial nanochannels,as well as the smart nanofluidic gating system controlled by the water wettability.     

MD模拟方法研究圆柱形纳米微孔的吸附平衡

本文用MD（分子动力学）模拟方法对圆柱形纳米微孔中的Lennard-Jones流体的物理吸附平衡及界面现象进行了研究。模拟中引入新型势模型,采用了计数法计算平衡压力,预测了在不同孔径下（直径为 3～5nm）的吸附等温线,分析了毛细凝聚理论用于纳米微孔吸附的局限性。并比较了同一纳米尺度的窄缝形微孔和圆柱形微孔吸附的差异。     

聚丙烯腈基碳纤维原丝在纺丝过程中纳米孔变化规律与机理研究

应用小角X射线散射等方法, 系统、定量地测试表征了聚丙烯腈基碳纤维原丝中纳米孔的尺寸、形状、体积分数、单位体积中纳米孔绝对数量以及纤维总孔洞率等形态结构参量, 并对这些参量在水洗、水洗牵伸、热致密化、高压蒸汽牵伸及热稳定化等工艺过程中的变化规律及原因进行了研究. 结果表明, 纺丝过程中牵伸及高温热处理均可使纤维总孔洞率逐步下降. 纳米孔尺寸体积分数V_i测试表明, 对于小于10 nm³的小纳米孔和大于10³ nm³的较大纳米孔, 两者的V_i在纺丝初期水洗牵伸工艺中分别为0.217和0.369, 而在纺丝后期热稳定化处理后发生大幅度改变, 分别为0.948 与0.015. 其原因并不是在高压蒸汽牵伸及热稳定处理中较小纳米孔含量的增加, 而是较大纳米孔含量的大幅度减少. 纳米孔形状研究表明, 纺丝工艺中的多次牵伸处理均使纳米孔的长短轴比加大, 而大于玻璃化温度的热处理均使纳米孔长短轴比收缩, 并且对于较小纳米孔来说这种收缩更为显著.     

Metal nanorod production in silicon matrix by electroless process

Metal filled Si nanopores, that is, metal nanorods in an Si matrix, are produced by an electroless process that consists of three steps: (1) electroless displacement deposition of metal nanoparticles from a metal salt solution containing HF; (2) Si nanopore formation by metal-particle-enhanced HF etching; and (3) metal filling in nanopores by autocatalytic electroless deposition. Ag nanoparticles produce Si nanopores whose sizes are a few tens of nm in diameter and ca. 50 nm deep. Au nanoparticles produce finer and straighter nanopores on Si than the Ag case. These nanopores are filled with a Co or a Co-Ni alloy by autocatalytic deposition using dimethylamine-borane as a reducing agent. Phosphinate can be used as a reducing agent for the Au-deposited-and-pore-formed Si. The important feature of this process is that the metal nanoparticles, that is, the initiation points of the autocatalytic metal deposition, are present on the bottoms of the Si nanopores.     

Water and Ion Permeation through Electrically Charged Nanopore

The behaviour of water and small solutes in confined geometries is important to a variety of chemical and nanofluidic applications. Here we investigate the permeation and distribution of water and ions in electrically charged carbon cylindrical nanopore during the osmotic process using molecular dynamics simulations. In the simulations, charges are distributed uniformly on the pores with diameter of 0.9 nm. For nanopores with no charge or a low charge, ions are difficult to enter. With the increasing of charge densities on the pores, ions will appear inside the nanopores because of the large electronic forces between the ions and the charged pores. Different ion entries induce varying effects on osmotic water flow. Our simulations reveal that the osmotic water can flow through the negatively charged pore occupied by K^＋ ions, while water flux through the positively charged pores will be disrupted by Cl^- ions inside the pores. This may be explained by the different radial distributions of K^＋ ions and Cl^- ions inside the charged nanopores.     

DNA in nanopores: counterion condensation and coion depletion

Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule inside. In the presence of DNA, the counterions condense on the stretched macromolecule effectively neutralizing it, and nearly complete depletion of coions from the pore is observed. The implications of our results for experiments on DNA translocation through alpha-hemolysin nanopores are discussed.     

Spiking sychronization regulated by noise in three types of Hodgkin—Huxley neuronal networks

In this paper,we study spiking synchronization in three different types of Hodgkin-Huxley neuronal networks,which are the small-world,regular,and random neuronal networks.All the neurons are subjected to subthreshold stimulus and external noise.It is found that in each of all the neuronal networks there is an optimal strength of noise to induce the maximal spiking synchronization.We further demonstrate that in each of the neuronal networks there is a range of synaptic conductance to induce the effect that an optimal strength of noise maximizes the spiking synchronization.Only when the magnitude of the synaptic conductance is moderate,will the effect be considerable.However,if the synaptic conductance is small or large,the effect vanishes.As the connections between neurons increase,the synaptic conductance to maximize the effect decreases.Therefore,we show quantitatively that the noise-induced maximal synchronization in the Hodgkin-Huxley neuronal network is a general effect,regardless of the specific type of neuronal network.     

Mechanical properties of sorbents depending on nanopore sizes

The effect of the nanopore size on the mechanical properties of a porous carbon material with the density of 1.4 g/сm³ is discussed. The atomistic models of porous carbon materials depending on the nanopore size are constructed. The numerical experiments are implemented with using the molecular mechanical method based on the Brenner potential. The Young’s moduli are evaluated for porous carbon structures at certain nanopore dimensions and are found to decrease with the enlarging nanopores.     

Electrokinetic transport of nanoparticles to opening of nanopores on cell membrane during electroporation

Nanoparticle transport to the opening of the single nanopore created on the cell membrane during the electroporation is studied. First, the permeabilization of a single cell located in a microchannel is investigated. When the nanopores are created, the transport of the nanoparticles from the surrounding liquid to the opening of one of the created nanopores is examined. It was found that the negatively charged nanoparticles preferably move into the nanopores from the side of the cell membrane that faces the negative electrode. Opposite to the electro-osmotic flow effect, the electrophoretic force tends to draw the negatively charged nanoparticles into the opening of the nanopores. The effect of the Brownian force is negligible in comparison with the electro-osmosis and the electrophoresis. Smaller nanoparticles with stronger surface charge transport more easily to the opening of the nanopores. Positively charged nanoparticles preferably enter the nanopores from the side of the cell membrane that faces the positive electrode. On this side, both the electrophoretic and the electro-osmotic forces are in the same directions and contribute to bring the positively charged particles into the nanopores.