Transport of hydrated nitrate and nitrite ions through graphene nanopores in aqueous medium

Nitrate () and nitrite () ions are naturally occurring inorganic ions that are part of the nitrogen cycle. High doses of these ions in drinking water impose a potential risk to public health. In this work, molecular dynamics simulations are carried out to study the passage of nitrate and nitrite ions from water through graphene nanosheets (GNS) with hydrogen-functionalized narrow pores in presence of an external electric field. The passage of ions through the pores is investigated through calculations of ion flux, and the results are analyzed through calculations of various structural and thermodynamic properties such as the density of ions and water, ion–water radial distribution functions, two-dimensional density distribution functions, and the potentials of mean force of the ions. Current simulations show that the nitrite ions can pass more in numbers than the nitrate ions in a given time through GNS hydrogen-functionalized pore of different geometry. It is found that the nitrite ions can permeate faster than the nitrate ions despite the former having higher hydration energy in the bulk. This can be explained in terms of the competition between the number density of the ions along the pore axis and the free energy barrier calculated from the potential of mean force. Also, an externally applied electric field is found to be important for faster permeation of the nitrite over the nitrate ions. The current study suggests that graphene nanosheets with carefully created pores can be effective in achieving selective passage of ions from aqueous solutions.     

Atomic force microscopy imaging and electrical recording of lipid bilayers supported over microfabricated silicon chip nanopores: lab-on-a-chip system for lipid membranes and ion channels

We describe a silicon chip-based supported bilayer system to detect the presence of ion channels and their electrical conductance in lipid bilayers. Nanopores were produced in microfabricated silicon membranes by electron beam lithography as well as by using a finely focused ion beam. Thermal oxide was used to shrink pore sizes, if necessary, and to create an insulating surface. The chips with well-defined pores were easily mounted on a double-chamber plastic cell recording system, allowing for controlling the buffer conditions both above and below the window. The double-chamber system allowed using an atomic force microscopy (AFM) tip as one electrode and inserting a platinum wire as the second electrode under the membrane window, to measure electrical current across lipid bilayers that are suspended over the pores. Atomic force imaging, stiffness measurement, and electrical capacitance measurement show the feasibility of supporting lipid bilayers over defined nanopores: a key requirement to use any such technique for structure-function study of ion channels. Online addition of gramicidin, an ion-channel-forming peptide, resulted in electrical current flow across the bilayer, and the I-V curve that was measured using the conducting AFM tip indicates the presence of many conducting gramicidin ion channels.     

Solvation force, structure and thermodynamics of fluids confined in geometrically rough pores

The effect of periodic surface roughness on the behavior of confined soft sphere fluids is investigated using grand canonical Monte Carlo simulations. Rough pores are constructed by taking the prototypical slit-shaped pore and introducing unidirectional sinusoidal undulations on one wall. For the above geometry our study reveals that the solvation force response can be phase shifted in a controlled manner by varying the amplitude of roughness. At a fixed amplitude of roughness, a, the solvation force for pores with structured walls was relatively insensitive to the wavelength of the undulation, lambda for 2.3/=0.5. The predictions of the superposition approximation, where the solvation force response for the rough pores is deduced from the solvation force response of the slit-shaped pores, was in excellent agreement with simulation results for the structured pores and for lambda/sigma(ff)>/=7 in the case of smooth walled pores. Grand potential computations illustrate that interactions between the walls of the pore can alter the pore width corresponding to the thermodynamically stable state, with wall-wall interactions playing an important role at smaller pore widths and higher amplitudes of roughness.     

Estimation of diffusion parameters in functionalized silicas with modulated porosity. Part II: pore network modeling

In this work, the pore structure of those five (5) silicas SiO2-X (see Part I) which have suffered gradual functionalization with functional groups X of increasing length (X = psi, [triple bond]Si-H, [triple bond]Si-CH2OH, [triple bond]Si-(CH2)3OH, [triple bond]Si-(CH2)11CH3), is modeled as a three-dimensional cubic network of cylindrical pores. Those hybrids organic-inorganic SiO2-X samples are characterized by different extent of pore blocking effects. The pores of samples are represented in a 9 x 9 x 9 lattice by the nodes as well the bonds that are interconnected in a so-called dual site-bond model, DSBM, network. The pore network is developed using a Monte Carlo statistical method where the cylindrical pores (nodes and bonds) are randomly assigned into the lattice, until matching of the theoretical results to the experimental data of N2 adsorption-desorption measurements. Thus, a visual picture of the porous solid is possible. This realistic network is used next in order to study the steady-state gas transport (Knudsen gas-phase and viscous diffusion) properties for the examined materials and how flow processes depend on the morphology of the pore structure. The pore diffusivity Dp and total permeability P of each porous medium is determined based on theoretical calculations and the structural statistical parameters, such as porosity epsilonp, tortuosity factor tau and connectivity c of pores is discussed with the corresponding experimental data described in Part I of this work. The results indicate clearly that the diffusion model made it possible to predict pore effective diffusivity in these porous media in very good agreement with the corresponding experimental results for all the examined solids (Part I). The pore diffusivity increases significantly as the value of the pore connectivity increases but the transport properties of the network are influenced strongly at lowest connectivity. Also the predicted tortuosity factor is related inversely to the extent of interconnection of pores in these solids, which indicates that the influence of pore branching to the tortuosity factor of the pore network decreases, as connectivity increases.     

丙烯聚合新催化剂的结构特征

用X射线衍射法测定了索尔维型丙烯聚合新催化剂的微晶粒大小为100A左右,比其它方法所制得的同类型催化剂微晶粒要小;并发现催化剂活性与微晶粒大小几乎成线性关系,微晶粒越小催化活性越高。 用ST-03型比表面、孔径分布测定仪研究了催化剂的孔结构。结果表明本催化剂具有较大的比表面和孔体积及粗细孔均备的优良孔结构,保证钛活性中心的充分利用,因而催化剂表现出较高的催化活性。     

Nucleation free energy of pore formation in an amphiphilic bilayer studied by molecular dynamics simulations

The formation of a pore in a membrane requires a considerable rearrangement of the amphiphilic molecules about to form the bilayer edge surrounding the pore, and hence is accompanied by a steep increase of the free energy. Recent rupture and conductance experiments suggest that this reshuffling process is also responsible for a small energy barrier that stabilizes "prepores" with diameters of less than 1 nm, rendering both the opening and closing of pores an activated process. We use the potential of mean constraint force method to study this free energy profile, as a function of pore radius, in a coarse grained bilayer model. The calculations show that the free energy rises by (15-20) kT during pore opening, making it an extremely rare nucleation event. Although we do not observe a barrier to pore closure, the results do make the existence of such a barrier plausible. For larger pores we find a smooth transition to Litster's model, from which a line tension coefficient of about 3.7 x 10(-11) J m(-1) is deduced.     

Monte Carlo Calculations of Polymer Adsorption at the Entrance of Cylindrical Pores in Flat Adsorbing Surfaces

The influence of surface interactions on the conformation of flexible polymers partially confined inside narrow cylindrical pores in a flat surface is studied above the critical adsorption energy in a good solvent. We use a static configurational bias computational sampling method to calculate the adsorption free energy and the radius of gyration components parallel and perpendicular to the pore axis as a function of the polymer center of mass position at different degrees of confinement. We find strong free‐energy minima just in front of the pore entry for all degrees of confinement studied. At the location of the free‐energy minimum, polymers are partially adsorbed inside the pore and on the outer solid surface and adopt “drawing pin”‐like conformations. A distinct maximum in the average loop length at the pore entry indicates that the polymer bridges the pore entry of small pores.     

Repulsive interface forces in overlapping electric double layers in electrolyte solutions

The historical development of the problem of the electric interaction of particles in electrolyte solutions is comprehensively discussed. The existing approaches are divided into force-based methods, where the mechanical (ponderomotive) forces of the electric field are directly calculated, and energy-based methods calculating the free energy of the colloid system (at least the part of the free energy which is determined by the repulsive forces of electrical nature). The fundamental works of Langmuir, Derjaguin, Levine, Verwey and Overbeek are discussed in detail. At the same time, new original methods are proposed: the method of effective displacements; the formula of free energy of overlapping double layers.Special attention is paid to the analysis of electrostriction forces in liquids, particularly in electric double layers. The non-contradictory application of the concepts of classic macroelectrostatics is shown to result in the need to take into account electrostriction forces in overlapping double layers. The main formulas are given for force and energy of repulsion in flat surfaces with a constant density of the electric charge on them. These formulas are derived with electrostriction forces taken into account. A number of the theoretical results are new.Some experiments are discussed in measuring repulsive forces in colloid systems. A qualitative agreement is established between the experimental results of Ottewill et al. and the theory of electrostriction forces in double layers.     

Modeling peptide binding to anionic membrane pores

Peptide‐induced pore formation in membranes can be dissected into two steps: pore formation and peptide binding to the pore. A computational method is proposed to study the second step in anionic membranes. The electrostatic potential is obtained from numerical solutions to the Poisson–Boltzmann equation and is then used in conjunction with IMM1 (implicit membrane model 1). A double charge layer model is used to incorporate the effects of the membrane dipole potential. Inhomogeneity of the charge density in the pore, characterized by explicit membrane simulations of toroidal pores, is included in the model. This approach was applied to two extensively studied peptides, magainin and melittin. In agreement with previous work, binding to toroidal pores is more favorable than binding to the flat membrane. The dependence of binding energy on anionic content exhibits different patterns for the two peptides, in correlation with the different lipid selectivity that has been observed experimentally. © 2013 Wiley Periodicals, Inc.     

基体石墨的孔隙结构及其对单质Ag扩散的影响

高温气冷堆燃料元件的基体石墨是一种多孔复合材料,是燃料元件的主要组成部分,其结构影响燃料元件的性能和裂变产物在燃料元件中的扩散。 本文利用压汞法表征基体石墨的孔隙结构,并讨论了基体石墨制备工艺中最大压制压强与热处理过程对孔隙结构的影响。 结果表明,基体石墨大孔孔径分布为6001900 nm,高温热处理使基体石墨的总孔隙率、中值孔径、大孔孔容均减小;基体石墨热处理样品的大孔孔容随最大压制压强的增加而呈线性减少,热处理过程单质Ag在石墨基体中的扩散速度与大孔孔容变化具有正相关性。     

Poly(N-isopropylacrylamide) grafted into nanopores: Thermo-responsive behaviour in the presence of different salts

Surface initiated polymerization of N(isopropylacrylamide) (NIPAM) was performed by controlled radical polymerization on PET track-etched membranes presenting two different pore diameters (narrow pores: ∼80 nm and large pores: ∼330 nm). The opening and closing characteristics of the resulting PNIPAM-g-PET membranes were investigated by conductometric measurements carried out at different temperatures below and above the LCST of PNIPAM and in the presence of different salts. Depending on the membrane pore size, two types of permeation control mechanisms are observed. In large pore membranes, expanded PNIPAM chains conformations result in reduced effective pore size and therefore lower permeabilities relative to collapsed macromolecules chain conformations. In contrast, in narrow pore membranes, the expanded PNIPAM brush presents greater degrees of hydration in the surface layer and therefore gives rise to higher permeabilities than the collapsed conformation. In this situation, the overall permeability is thus comparable to that of a hydrogel membrane.     

A trapped water network in nanoporous material: the role of interfaces

The infrared spectra of water confined in well controlled pore glasses were recorded as a function of the pore size ranging from 8 to 320 nm and in the 30-4000 cm(-1) spectral range using the ATR technique. The experiments prove that even in the large pores, the water network is significantly perturbed. The energy of the connectivity (or hindered translation) band (around 150 cm(-1)) is found to increase when the pore size decreases, indicating that confinement increases the H-bonding between neighbouring water molecules. Moreover, a drastic decrease of the FWHM of the connectivity band was observed upon confinement. This can be related to some ordering induced by the rigid walls of the pores. Furthermore, the partial filling of pores causes a significant modification to the water network, resembling heating of the trapped liquid and suggesting a role played by the water/air interface.     

Dynamic strength of molecularly bonded surfaces

This study reports a theoretical analysis of the forced separation of two adhesive surfaces linked via a large number of parallel noncovalent bonds. To describe the bond kinetics, we implement a three-state reaction model with kinetic rates obtained from a simple integral expression of the mean first passage time for diffusive barrier crossing in a pulled-distance-dependent potential. We then compute the rupture force for the separation of adhesive surfaces at a constant rate. The results correspond well with a Brownian dynamics simulation of the same system. The separation rate relative to the intrinsic relaxation time of the bonds defines three loading regimes and the general dependence of the adhesion on kinetic or thermodynamic parameters of the bonds. In the equilibrium regime, the rupture force asymptotically approaches the equilibrium rupture force, which increases linearly with the equilibrium bond energy. In the near-equilibrium regime, the rupture force increases with the separation rate and increasingly correlates with the bond rupture barrier. In the far-from-equilibrium regime where rebinding is irrelevant, the rupture force varies linearly with the rupture barrier.     

Investigation of dynamic streaming potential by dimensional analysis

The theory of streaming potential at sinusoidal flow of liquid in a porous medium is a convenient and fruitful tool for determination of the interface properties of materials and also for construction of apparatus for zeta potential measurements and electrokinetic transducers. An investigation of the dynamic streaming potential by the method of dimensional analysis is presented. This method provides a wider approach to the problem under consideration. As a result, relationships between streaming potential in a porous medium and mechanical quantities are established. These quantities include pressure gradient in a liquid inside pores and capillaries, acceleration of capillaries, and the solid part of a porous medium, and the viscous friction force the liquid exerts on the solid part. The corresponding formulas for streaming potential are presented. The relationship between the streaming potential and viscous friction force does not depend on the frequency of oscillation and pore size. All these formulas in particular cases are transformed to known formulas for the streaming potential.     

Nonlinear current-voltage relationship of the plasma membrane of single CHO cells

The application of electric field pulses to Chinese Hamster Ovary (CHO) cells causes membrane electroporation (MEP). If a voltage or current ramp is applied to the cellular membrane of a single CHO cell, the membrane conductance increases nonlinearly with field strength reaching saturation. In particular, the kinetics of the induced conductance changes represents the data basis for the interpretation in terms of underlying structural changes. The current/voltage characteristic is found to be continuous, but displays occasionally a sharp increase in the conductance. The step-like increases are interpreted to reflect the formation of one (or more) larger pore(s). The analysis of current clamp data yields pores of radius (r(p)) in the range of 2.5< or =r(p)/nm< or =20; the pores of the voltage clamp data are in the range of 2.5< or =r(p)/nm< or =55. The larger pores occur predominantly during hyperpolarising and less frequently during depolarising conditions, respectively. The different kinetics of pore formation in the hyperpolarising condition, where the inward field increases, and the depolarising condition, where the inward field first decreases and then increases in the opposite direction, suggests structural asymmetry with respect to the direction of the electric membrane field. At the required higher voltage, the effect of the resting potential is negligibly small.     

Advective flow in a sludge floc

The interior of sludge floc is highly heterogeneous, while the large pores in the floc control the advective flow. This work for the first time numerically details fluid flow and mass transfer processes in pores of activated sludge floc. The dimensionless permeabilities and mass dispersion coefficients were contoured against pore size ratio and the floc Reynolds number. With a pore size less than 20% of the floc size, the commonly adopted homogeneous model overestimates the floc permeability, and pore velocity is less than 2% of the bulk velocity. This is particularly true for flocs with low porosity. Although the convective flux is low, the dispersive mass transfer rate can be much higher than the diffusional rate, attributable to the strong Taylor dispersion effect. The three-dimensional pore structures in waste activated-sludge floc were identified using confocal laser scanning microscope (CLSM) images. Large pores were used to numerically estimate the permeability and dispersion coefficient for these pores. The permeability and the dispersion coefficient of the tortuous pores can be one order of magnitude lower than those for the equivalent straight pores. Besides the dispersion effect, the pore tortuosity appeared as the most important geometrical factor retarding the advective flow in the sludge pores. In addition, the small side pores connected to the large pore had only a mild effect on the flow process, and can be neglected in analysis.     

Numerical Study of Pore Sizes Distribution in Gels

We introduce a new numerical technique for the calculation of the pore size distribution in two-dimensional disordered systems. Our method is based on a triangulation technique which allows a closer measurement of pores surface without any morphological hypothesis.In this work, we focus our calculations in simulated gels. Such materials are modeled in two different conditions: by means of the Diffusion-Limited and Reaction-Limited Cluster-cluster Aggregation algorithms, DLCA and RLCA, respectively. In both situations, when the particles concentration decreases, the average pores size increases. The more compact cluster in RLCA, compared with DLCA, is consistent with the pore size distribution we have calculated. The simulated mean pore size is quantitatively in agreement with experimental data from literature.     

Activation energy of single-stranded DNA moving through cross-linked polyacrylamide gels at 300 V/cm effect of temperature on sequencing rate in high-electric-field capillary gel electrophoresis

In DNA sequencing, single-stranded DNA fragments are separated by gel electrophoresis. This separation is based on a sieving mechanism where DNA fragments are retarded as they pass through pores in the gel. In this paper, we present the mobility of DNA sequencing fragments as a function of temperature; mobility is determined in 4% T LongRanger gels at an electric field of 300 V/cm. The temperature dependence is compared with the predictions of the biased reptation model. The model predicts that the fragment length for the onset of biased reptation with stretching increases with the square of temperature; the data show that the onset of biased reptation with stretching decreases with temperature. Biased reptation fails to model accurately the temperature dependence of mobility. We analyzed the data and extracted the activation energy for passage of sequencing fragments through the gel. For fragments containing less than ca. 200 bases, the activation energy increases linearly with the number of bases at a rate of 25 J/mol per base; for longer fragments, the activation energy increases at a rate of 6.5 J/mol per base. This transition in the activation energy presumably reflects a change in conformation of the DNA fragments; small fragments exist in a random coil configuration and larger fragments migrate in an elongated configuration.     

Simulation of pore formation in lipid bilayers by mechanical stress and electric fields

We describe computer simulations of pore formation and membrane rupture of phospholipid bilayers under mechanical and electrical stress. On the nanosecond simulation time scale, pores are induced by a lateral pressure exceeding -200 bar or by an applied electric field of 0.5 V/nm.