Investigation of entrance and exit effects on liquid transport through a cylindrical nanopore

The entrance and exit effects on liquid transport through a nano-sized cylindrical pore under different solid wall-liquid interactions were studied by comparing molecular dynamics (MD) results of a finite length nanopore in a membrane with those of an infinite length one. The liquid transport through a finite length nanopore in a membrane was carried out by using a pressure-driven non-equilibrium molecular dynamics (NEMD) method proposed by Huang et al. [C. Huang, K. Nandakumar, P. Choi and L. W. Kostiuk, J. Chem. Phys., 2006, 124, 234701]. The fluid motion through an infinite length nanopore, which had the same cross-stream dimension as the finite length channel in the membrane, but with periodic boundary conditions in the stream-wise direction, was carried out by using the external-field driven NEMD approach [J. Koplik, J. R. Bavanar and J. F. Willemsen, Phys. Rev. Lett., 1988, 60, 1282]. The NEMD results show that the pressure and density distributions averaged over the channel in the radial direction in both finite and infinite length channels are similar, but the radial distributions of the stream-wise velocity were significantly different when the solid wall was repulsive. The entrance and exit effects lead to a decrease in flow rate at about 39% for the repulsive wall and 6% for the neutral-like wall.     

Molecular dynamics simulation of a pressure-driven liquid transport process in a cylindrical nanopore using two self-adjusting plates

Fluid transport through a nanopore in a membrane was investigated by using a novel molecular dynamics approach proposed in this study. The advantages of this method, relative to dual-control-volume grand-canonical molecular dynamics method, are that it eliminates disruptions to the system dynamics that are normally created by inserting or deleting particles from control volumes, and that it functions well for dense systems due to the number of particles being fixed in the system. Using the proposed method, we examined liquid argon transport through a nanopore by performing nonequilibrium molecular dynamics (NEMD) simulations under different back pressures. Validation of the code was performed by comparing simulation results to published experimental data obtained under equilibrium conditions. NEMD results show that constant pressure difference across the membrane was readily achieved.     

Direct numerical simulation of electrokinetic translocation of a cylindrical particle through a nanopore using a Poisson-Boltzmann approach

Nanopore-based sensing of single molecules is based on a detectable change in the ionic current arising from the electrokinetic translocation of individual nanoparticles through a nanopore. In this study, we propose a continuum-based model to investigate the dynamic electrokinetic translocation of a cylindrical nanoparticle through a nanopore and the corresponding ionic current response. It is the first time to simultaneously solve the Poisson-Boltzmann equation for the ionic concentrations and the electric field contributed by the surface charges of the nanopore and the nanoparticle, the Laplace equation for the externally applied electric field, and the modified Stokes equations for the flow field using an arbitrary Lagrangian-Eulerian method. Current blockade due to the particle translocation is predicted when the electric double layers (EDLs) of the particle and the nanopore are not overlapped, which is in qualitative agreement with existing experimental observations. Effects due to the electric field intensity imposed, the EDL thickness, the nanopore's surface charge, the particle's initial orientation and lateral offset from the nanopore's centerline on the particle translocation including both translation and rotation, and the ionic current response are comprehensively investigated. Under a relatively low electric field imposed, the particle experiences a significant rotation and a lateral movement. However, the particle is aligned with its longest axis parallel to the local electric field very quickly due to the dielectrophoretic effect when the external electric field is relatively high.     

Polymer translocation through a nanopore: a two-dimensional Monte Carlo study

We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. To overcome the entropic barrier without artificial restrictions, we consider a polymer which is initially placed in the middle of the pore and study the escape time tau required for the polymer to completely exit the pore on either end. We find numerically that tau scales with the chain length N as tau approximately N(1+2nu), where nu is the Flory exponent. This is the same scaling as predicted for the translocation time of a polymer which passes through the nanopore in one direction only. We examine the interplay between the pore length L and the radius of gyration R(g). For LR(g), we find tau approximately N. In addition, we numerically find the scaling function describing crossover between short and long pores. We also show that tau has a minimum as a function of L for longer chains when the radius of gyration along the pore direction R( parallel) approximately L. Finally, we demonstrate that the stiffness of the polymer does not change the scaling behavior of translocation dynamics for single-segment dynamics.     

Forces between cylindrical nanoparticles in a liquid crystal

Using classical density functional theory, the forces between two cylindrical nanoparticles in a liquid crystal solvent are calculated. Both the nematic and isotropic phases of the solvent are considered. In the nematic phase, the interaction is highly anisotropic. At short range, changes in the defect structure around the cylinders leads to a complex interaction between them. In the isotropic phase, an attractive interaction arises due to overlap between halos of ordered fluid adsorbed on the surfaces of the cylinders.     

Simulation study on the translocation of a partially charged polymer through a nanopore

The translocation of a partially charged polymer through a neutral nanopore under external electrical field is studied by using dynamic Monte Carlo method on a simple cubic lattice. One monomer in the polymer is charged and it suffers a driving force when it locates inside the pore. Two time scales, mean first passage time τ(FP) with the first monomer restricted to never draw back into cis side and translocation time τ for polymer continuously threading through nanopore, are calculated. The first passage time τ(FP) decreases with the increase in the driving force f, and the dependence of τ(FP) on the position of charged monomer M is in agreement with the theoretical results using Fokker-Planck equation [A. Mohan, A. B. Kolomeisky, and M. Pasquali, J. Chem. Phys. 128, 125104 (2008)]. But the dependence of τ on M shows a different behavior: It increases with f for M < N/2 with N the polymer length. The novel behavior of τ is explained qualitatively from dynamics of polymer during the translocation process and from the free energy landscape.     

Chaperone-assisted translocation of a polymer through a nanopore

Using Langevin dynamics simulations, we investigate the dynamics of chaperone-assisted translocation of a flexible polymer through a nanopore. We find that increasing the binding energy ε between the chaperone and the chain and the chaperone concentration N(c) can greatly improve the translocation probability. Particularly, with increasing the chaperone concentration a maximum translocation probability is observed for weak binding. For a fixed chaperone concentration, the histogram of translocation time τ has a transition from a long-tailed distribution to a gaussian distribution with increasing ε. τ rapidly decreases and then almost saturates with increasing binding energy for a short chain; however, it has a minimum for longer chains at a lower chaperone concentration. We also show that τ has a minimum as a function of the chaperone concentration. For different ε, a nonuniversal dependence of τ on the chain length N is also observed. These results can be interpreted by characteristic entropic effects for flexible polymers induced by either the crowding effect from a high chaperone concentration or the intersegmental binding for the high binding energy.     

Molecular dynamics study of ionic liquid confined in silicon nanopore

Russian Journal of Physical Chemistry A - Molecular dynamics simulations was carried to investigate the structure and dynamics of [BMIM][PF6] ionic liquid (IL) confined inside a slit-like silicon...     

Driven translocation of semiflexible polyelectrolyte through a nanopore

The influence of the chain stiffness on the translocation of semiflexible polyelectrolyte through a nanopore is investigated using Langevin dynamics simulations. Results show that the translocation time τ increases with the bending modulus k_θ because of the increase of viscous drag forces with k_θ. We find that the relation between τ and k_θ, the asymptotic behavior of τ on the polyelectrolyte length N, and the scaling relation between τ and the driving force f are dependent on k_θ and N. Our simulation results show that the semiflexible polyelectrolyte chain can be regarded as either a flexible polyelectrolyte at small k_θ or large N where its radius of gyration R_G is larger than the persistence length L_p or a stiff polyelectrolyte at large k_θ or short N where R_G < L_p. Results also show that the out‐of‐equilibrium effect during the translocation becomes weak with increasing k_θ. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 912–921     

Differential capacitance of liquid/liquid interfaces of finite thicknesses: a finite element study

Finite element simulations were used to investigate the effect of a smooth variation of permittivity across a polarized liquid/liquid interface on the differential capacitance. The results show that a relative permittivity profile can account for the variation of ion solvation in the interfacial region, and therefore upon the diffuse double layer itself. The width and the symmetry of this profile across the interface are shown to be crucial parameters for interfacial distributions and fitting of capacitance data has been used to estimate the width of the interfacial region.     

Modeling and simulation of nanoparticle separation through a solid-state nanopore

Recent experimental studies show that electrokinetic phenomena such as electroosmosis and electrophoresis can be used to separate nanoparticles on the basis of their size and charge using nanopore‐based devices. However, the efficient separation through a nanopore depends on a number of factors such as externally applied voltage, size and charge density of particle, size and charge density of membrane pore, and the concentration of bulk electrolyte. To design an efficient nanopore‐based separation platform, a continuum‐based mathematical model is used for fluid. The model is based on Poisson–Nernst–Planck equations along with Navier–Stokes equations for fluid flow and on the Langevin equation for particle translocation. Our numerical study reveals that membrane pore surface charge density is a vital parameter in the separation through a nanopore. In this study, we have simulated high‐density lipoprotein (HDL) and low‐density lipoprotein (LDL) as the sample nanoparticles to demonstrate the capability of such a platform. Numerical results suggest that efficient separation of HDL from LDL in a 0.2 M KCL solution (resembling blood buffer) through a 150 nm pore is possible if the pore surface charge density is ～ ?4.0 mC/m². Moreover, we observe that pore length and diameter are relatively less important in the nanoparticle separation process considered here.     

Single molecule measurements of DNA transport through a nanopore

We examined the voltage-driven movement of single-stranded DNA molecules in a membrane channel or "nanopore". Using single channel recording methods and a statistical analysis of many single molecule events, we determined how voltage influences capture and translocation in the nanopore. We verified that the mean time between capture events follows a simple exponential distribution, whereas the translocation times follow a unique distribution that is partly Gaussian and partly exponential. Measurements of polymer sequence effects demonstrated that translocation duration is heavily influenced by specific or nonspecific purine-channel interactions. The single molecule approach we used revealed molecular interactions that can influence both capture rates and translocation velocities in a manner that enriches naive barrier crossing models.     

Theoretical study on the translocation of partially charged polymers through nanopore

The translocation time τ of partially charged polymers through a neutral nanopore is calculated using Fokker–Planck equation with adsorbing–adsorbing boundary conditions. For the polymer with one charged monomer, we find that τ is dependent on the position of the charged monomer and on the magnitude of the driving force f inside the nanopore. When the charge is located at the front half of the polymer chain, τ is larger than that of neutral polymer and increases with f. When the charge is located at the back half, it is smaller than that of the neutral polymer and decreases with increasing f. We have also studied the behavior of a symmetrical polymer with two like charges located symmetrically in the chain and that of an asymmetrical polymer with two unlike charges. Moreover, we have calculated the translocation time for a general condition of polymer with two randomly distributed charges. All results show that τ is dependent on the positions of charges in the polymer chain and on the magnitude of the driving force. The results can be explained qualitatively by the free‐energy landscape of polymer translocation. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 1017–1025     

Electroosmotic flow through porous media: cylindrical and annular models

Electroosmotic flow rates through porous media are predicted through the cylindrical and annular geometrical models. Differences in the results obtained from the two models are compared and discussed by making reference to the electrokinetic remediation of contaminated soil. In the annular-model case, when the electrical potential on the outer wall is less than on the inner wall and/or the double-layer thickness is much shorter than the outer radius, a maximum flux is predicted at some outer-to-inner-radii ratio. At a given soil porosity, the cylindrical model predicts a higher flow rate than the annular model, and the difference becomes increasingly more pronounced as the radii ratio approaches unity, which corresponds to a low-porosity soil.     

Dynamics of polymer translocation into a circular nanocontainer through a nanopore

Using Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a circular nanocontainer through a nanopore under a driving force F. We observe that the translocation probability initially increases and then saturates with increasing F, independent of φ, which is the average density of the whole chain in the nanocontainer. The translocation time distribution undergoes a transition from a Gaussian distribution to an asymmetric distribution with increasing φ. Moreover, we find a nonuniversal scaling exponent of the translocation time as chain length, depending on φ and F. These results are interpreted by the conformation of the translocated chain in the nanocontainer and the time of an individual segment passing through the pore during translocation.     

Water flow through polymeric and nonaqueous liquid membranes

Osmotic and isotopic water flows through polymeric and nonaqueous liquid membranes have been measured. The polymeric membranes were of the polyethylene–styrene graft copolymer type containing sulfonic acid groups. The nonaqueous liquid membranes were water-saturated 1-butanol and benzene. Osmotic water flux through both types of membranes was larger than isotopic (THO) water flux. Using these data, values for the equivalent pore radius for these membranes have been derived. The significance of such values has been briefly discussed.     

Memory effects during the unbiased translocation of a polymer through a nanopore

Through a detailed Langevin dynamics simulation study, the role of memory effects during unbiased translocation is explored. Tests are devised to uncover the presence of memory effects by directly measuring forward/backward-correlated motion as well as the associated change in the dynamics. Conducting these tests at low and high viscosities, a range of behaviours across different time scales is revealed: short-time forward correlations at all viscosities, quasi-static behaviour at low viscosity, and long-time backward correlations at high viscosity. By applying these tests at different portions of the translocation process, these memory effects are also shown to vary as translocation proceeds. Combining this information with standard measurements, a physical picture of unbiased translocation as the diffusion of a local minimum is proposed.     

Hydration repulsion between membranes and polar surfaces: Simulation approaches versus continuum theories

A review of various computer simulation approaches for the study of the hydration repulsion between lipid membranes and polar surfaces is presented. We discuss different methods and compare their advantages and limitations. We consider interaction pressures, interaction thermodynamics, and interaction mechanisms. We take a close look at the influence of the experimental boundary conditions and at repulsion mechanisms due to the unfavorable overlap of interfacial water layers. To this end, we analyze several distinct water order parameters in simulations of interacting polar surfaces and compare the results to the predictions of simple continuum theories.     

Solvent effects on NMR isotropic shielding constants. a comparison between explicit polarizable discrete and continuum approaches

The gas-to-aqueous solution shifts of the 17O and 13C NMR isotropic shielding constants for the carbonyl chromophore in formaldehyde and acetone are investigated. For the condensed-phase problem, we use the hybrid density functional theory/molecular mechanics approach in combination with a statistical averaging over an appropriate number of solute-solvent configurations extracted from classical molecular dynamics simulations. The PBE0 exchange-correlation functional and the 6-311++G(2d,2p) basis set are used for the calculation of the shielding constants. London atomic orbitals are employed to ensure gauge-origin independent results. The effects of the bulk solvent molecules are found to be crucial in order to calculate accurate solvation shifts of the shielding constants. Very good agreement between the computed and experimental solvation shifts is obtained for the shielding constants of acetone when a polarizable water potential is used. Supermolecular results based on geometry-optimized molecular structures are presented. We also compare the results obtained with the polarizable continuum model to the results obtained using explicit MM molecules to model the bulk solvent effect.     

Comparative study of different approaches for the flow injection-fourier transform infrared determination of toluene in gasolines

A single channel flow injection manifold has been employed to carry out the direct determination of toluene in gasolines by FT-IR without any sample pretreatment and by using different strategies. Toluene can be directly determined by measuring the absorbance at 728 cm(-1), using a base line established between 835 and 575 cm(-1); and in this case a limit of detection of 0.01% (v/v) can be obtained with a dynamic range up to 2% (v/v). In some cases it could be convenient to determine toluene by derivative flow-injection FT-IR in order to avoid matrix interferences in the analysis of some types of gasolines. Carrying out the first order derivative FI-FT-IR measurements on the 728 cm(-1) band between the peak at 731 and the valley at 725 cm(-1) toluene can be determined without problems in establishing the base line and with a limit of detection of 0.01% (v/v). On the other hand, the use of the quotient between the first order derivative absorbance values of toluene, at the 728 cm(-1) band, and benzene, at the 675 cm(-1) band, can be applied for the determination of toluene in gasolines in which benzene has been previously analyzed, avoiding problems related to the determination of the base line and making measurements independent of the spacer employed.