Electrokinetic ion and fluid transport in nanopores functionalized by polyelectrolyte brushes

Chemically functionalized nanopores in solid-state membranes have recently emerged as versatile tools for regulating ion transport and sensing single biomolecules. This study theoretically investigated the importance of the bulk salt concentration, the geometries of the nanopore, and both the thickness and the grafting density of the polyelectrolyte (PE) brushes on the electrokinetic ion and fluid transport in two types of PE brush functionalized nanopore: PE brushes are end-grafted to the entire membrane surface (system I), and to its inner surface only (nanopore wall) (system II). Due to a more significant ion concentration polarization (CP), the enhanced local electric field inside the nanopore, the conductance, and the electroosmotic flow (EOF) velocity in system II are remarkably smaller than those in system I. In addition to a significantly enhanced EOF inside the nanopore, the direction of the flow field near both nanopore openings in system I is opposite to that of EOF inside the nanopore. This feature can be applied to regulate the electrokinetic translocation of biomolecules through a nanopore in the nanopore-based DNA sequencing platform.     

Electrically tunable solid-state silicon nanopore ion filter

We show that a nanopore in a silicon membrane connected to a voltage source can be used as an electrically tunable ion filter. By applying a voltage between the heavily doped semiconductor and the electrolyte, it is possible to invert the ion population inside the nanopore and vary the conductance for both cations and anions in order to achieve selective conduction of ions even in the presence of significant surface charges in the membrane. Our model based on the solution of the Poisson equation and linear transport theory indicates that in narrow nanopores substantial gain can be achieved by controlling electrically the width of the charge double layer.     

Nanopore/electrode structures for single-molecule biosensing

Biological and solid-state nanopores have recently attracted much interest as ultrafast DNA fragment sizing and sequencing devices. Their potential however goes far beyond DNA sequencing. In particular, nanopores offer perspectives of single-molecule (bio)sensing at physiologically relevant concentrations, which is key for studying protein/protein or protein/DNA interactions. Integration of electrode structures into solid-state nanopore devices moreover enables control and fast switching of the pore properties, e.g. for active control of biopolymer transport through the nanopore. We present some of recent work in this area, namely the fabrication and characterization of nanopore/electrode architectures for single-(bio)molecule sensing. Specifically, we introduce a new technique to fabricate ultra-small metal nanopores with diameters smaller than 20 nm based on ion current feedback (ICF) controlled electrodeposition. It offers precise control of the pore conductance, is easily multiplexed, and can be extended to a wide range of different metals.     

Real gas transport in tapered noncircular nanopores of shale rocks

A model for gas transport in tapered noncircular nanopores of shale rocks with integrating real gas effect, molecular kinetic, and transport behavior was presented. The proposed model is well validated with experimental and simulation data, including six kinds of gases, under different pressures, and temperatures. Results show that neglect of real gas effect results in the misleading transport conductance. The adsorbed gas transport ratio and the ratio of area occupied by adsorbed gas increase along the length of nanopore. Pore proximity induces the faster gas transport and omitting pore proximity leads to the enlargement of the adsorbed gas‐dominated region. Increasing taper ratio (ratio of inlet size to outlet size) and aspect ratio weakens real gas effect and lowers free gas transport. Moreover, it lowers the total transport capacity of the nanopore, and the tapered circular nanopore owns the greatest transport capacity, followed by tapered square, elliptical, and rectangular nanopores. © 2017 American Institute of Chemical Engineers AIChE J, 63: 3224–3242, 2017     

Electrokinetic DNA transport in a nanopore membrane

There is tremendous current interest in transporting DNA molecules through nanopores. This interest stems from the possibility of using nanopores for characterization/sequencing, separation, and sensing of DNA. In the presence of a transmembrane electric field, typically used in such applications, DNA chains can be driven through the nanopore via the electrokinetic transport processes of electrophoresis and electroosmotic flow, as well as by diffusion. To our knowledge there have been no quantitative studies of the relative importance of the electrokinetic and diffusive components for DNA transport in a nanopore system. We describe such quantitative studies here. We report on the transport of a series of single-stranded homo-oligonucleotides made of thymidine bases through nanopores in a polycarbonate filter membrane. We show that when an ionic current is passed through the nanopores, transmembrane DNA electrophoresis is the dominant transport process. Finally, the pores in these membranes have conical constrictions at both membrane faces. The effect of this interesting pore geometry on DNA transport is also discussed.     

Slowing and controlling the translocation of DNA in a solid-state nanopore

DNA sequencing methods based on nanopores could potentially represent a low-cost and high-throughput pathway to practical genomics, by replacing current sequencing methods based on synthesis that are limited in speed and cost. The success of nanopore sequencing techniques requires the solution to two fundamental problems: (1) sensing each nucleotide of a DNA strand, in sequence, as it passes through a nanopore; (2) delivering each nucleotide in a DNA strand, in turn, to a sensing site within the nanopore in a controlled manner. It has been demonstrated that a DNA nucleotide can be sensed using electric signals, such as ionic current changes caused by nucleotide blockage at a constriction region in a protein pore or a tunneling current through the nucleotide-bridged gap of two nanoelectrodes built near a solid-state nanopore. However, it is not yet clear how each nucleotide in a DNA strand can be delivered in turn to a sensing site and held there for a sufficient time to ensure high fidelity sensing. This latter problem has been addressed by modifying macroscopic properties, such as a solvent viscosity, ion concentration or temperature. Also, the DNA transistor, a solid state nanopore dressed with a series of metal-dielectric layers has been proposed as a solution. Molecular dynamics simulations provide the means to study and to understand DNA transport in nanopores microscopically. In this article, we review computational studies on how to slow down and control the DNA translocation through a solid-state nanopore.     

Supramolecular Chemistry in the Biomembrane

The combination of supramolecular functional systems with biomolecular chemistry has been a fruitful exercise for decades, leading to a greater understanding of biomolecules and to a great variety of applications, for example, in drug delivery and sensing. Within these developments, the phospholipid bilayer membrane, surrounding live cells, with all its functions has also intrigued supramolecular chemists. Herein, recent efforts from the supramolecular chemistry community to mimic natural functions of lipid membranes, such as sensing, molecular recognition, membrane fusion, signal transduction, and gated transport, are reviewed.     

Study on the Characteristics of Gas Molecular Mean Free Path in Nanopores by Molecular Dynamics Simulations

This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale.     

In situ studies on the shrinkage and expansion of graphene nanopores under electron beam irradiation at temperatures in the range of 400–1200 °C

We report in situ studies on the shrinkage and expansion of graphene nanopores under electron beam irradiation at temperatures of 400–1200 °C using a thermal specimen holder in a transmission electron microscope. The shrinkage of nanopores of various sizes is observed. At all temperatures studied in the present work, nanopores with relatively small diameters could be fully closed. And at the low end of our temperature range, 400 °C, larger nanopores (those with a diameter of 10 nm) could also be closed completely. The nanopore shrinking process can be stopped by blocking the electron beam. We demonstrate an approach for tailoring the size of the graphene nanopore through a combination of electron beam irradiation and controlled heat.     

Multiscale modeling of ion transport in porous electrodes

Ion transport through nanoporous materials is of fundamental importance for the design and development of filtration membranes, electrocatalysts, and electrochemical devices. Recent experiments have shown that ion transport across porous materials is substantially different from that in individual pores. Here, we report a new theoretical framework for ion transport in porous materials by combining molecular dynamics (MD) simulations at nanopore levels with the effective medium approximation to include pore network properties. The ion transport is enhanced with the combination of strong confinement and dominating surface properties at the nanoscale. We find that the overlap of electric double layers and ion–water interaction have significant effects on the ionic distribution, flux, and conductance of electrolytes. We further evaluate the gap between individual nanopores and complex pore networks, focusing on pore size distribution and pore connectivity. This article highlights unique mechanisms of ion transport in porous materials important for practical applications.     

A capillary bundle model for the forced imbibition in the shale matrix with dual-wettability

The forced imbibition during hydraulic fracturing is one of the main mechanisms of oil production in shale oil reservoirs. However, the shale matrix has complex structures of nanopores and is rich in organic matters. The wettability of nanopores in organics matters is different from the nanopores in inorganic matters, and the characteristic of dual-wettability leads to complex mechanisms of forced imbibition. This paper proposes a model for describing the imbibition in a dual-wettability shale oil reservoir based on the capillary tube model. The external displacement pressure gradient is also considered to study the forced and spontaneous imbibition of hydraulic fracturing liquid into oil-wet organic nanopores and water-wet inorganic nanopores. The slip effect in organic nanopores and the boundary-layer effect in inorganic nanopores are considered in this model. The analytical expressions for describing the location of the oil–water imbibition front in an oil-wet organic nanopore and a water-wet inorganic nanopore are derived, respectively. The semi-analytical solution for predicting flow rate in a shale core with an external pressure gradient is given and demonstrated with a case study.     

Multifunctional three-dimensional nanodiamond-nanoporous alumina nanoarchitectures

Hybrid composite nanomaterials provide an attractive and versatile material platform for numerous emerging nano- and biomedical applications by offering the possibility to combine diverse properties which are impossible to obtain within a single material. In this work, we present the fabrication of novel hybrid diamond and amorphous diamond-like carbon (DLC) coated nanoporous alumina materials that exhibit multiple functionalities, such as high surface area, quasi-ordered nanopore structure, tunable surface chemistry and electrical conductivity, excellent biological, chemical and corrosion resistance. These multifunctional nanohybrid materials are fabricated using the plasma-induced carbonization method that effectively modifies the surface and the inside of the nanopores of anodic alumina, producing a homogenous ultrathin DLC protecting layer over the whole external and internal surfaces of the membranes. We demonstrate that the interplay between internal and external carbon supply is a critical factor for the formation of the ultrathin sp³-bonded carbon layer in the nanopores. This study brings new insights in the DLC growth mechanisms in confined nanospaces and opens new avenues to fabricate hybrid, chemically resistant and biocompatible carbon-coated nanoarchitectures on other inorganic supports.     

双响应性嵌段聚合物的纳米孔开关效应的计算机模拟

利用计算机模拟方法(耗散粒子动力学)研究了双响应性嵌段聚合物修饰的纳米孔的开关效应。通过在纳米孔内接枝具有温度和pH响应的嵌段聚合物(N-异丙基丙烯酰胺和丙烯酸),研究不同嵌段序列(即wall-PNIPAM-PAA或wall-PAA-PNIPAM)对纳米孔开关效应的影响,结果表明,只有wall-PNIPAM-PAA嵌段序列可以实现纳米孔在不同条件下的开关效应。同时还探究了接枝密度、链长和嵌段比例对纳米孔开关效应的影响,结果表明,中高等接枝密度、适合的链长和中等比例的嵌段比可以实现不同特征的纳米孔,用于控制纳米孔的开关效应。     

Nickel nanopore arrays as promising current collectors for constructing solid-state supercapacitors with ultrahigh rate performance

In this work, nickel nanopore arrays with a highly-oriented nanoporous structure inherited from porous alumina membranes were used as nanostructured current collectors for constructing ultrahigh rate solid-state supercapacitors. A thin layer of poly(3,4-ethylenedioxythiophene) (PEDOT) as electroactive materials was conformally coated onto nickel nanopores to form heterostructured electrodes. The as-prepared electrodes have a large specific surface area to ensure a high capacity, and the highly-oriented nanoporous structure of nickel nanopores reduces the ion transport resistance, allowing the ions in the solid-state electrolytes to quickly access the PEDOT surface during the fast charge-discharge process. As a result, the assembled solid-state supercapacitor in a symmetric configuration exhibits an ideal capacitive behavior and a superior rate capability even at an ultrahigh scan rate of 50 V·s⁻¹.     

Electrically facilitated translocation of protein through solid nanopore

Nanopores have been proven as versatile single-molecule sensors for individual unlabeled biopolymer detection and characterization. In the present work, a relative large nanopore with a diameter of about 60 nm has been used to detect protein translocation driven by a series of applied voltages. Compared with previous studied small nanopores, a distinct profile of protein translocation through a larger nanopore has been characterized. First, a higher threshold voltage is required to drive proteins into the large nanopore. With the increase of voltages, the capture frequency of protein into the nanopore has been markedly enhanced. And the distribution of current blockage events is characterized as a function of biased voltages. Due to the large dimension of the nanopore, the adsorption and desorption phenomenon of proteins observed with a prolonged dwell time has been weakened in our work. Nevertheless, the protein can still be stretched into an unfolded state by increased electric forces at high voltages. In consideration of the high throughput of the large nanopore, a couple of proteins passing through the nanopore simultaneously occur at high voltage. As a new feature, the feasibility and specificity of a nanopore with distinct geometry have been demonstrated for sensing protein translocation, which broadly expand the application of nanopore devices.     

Size evolution and surface characterization of solid-state nanopores in different aqueous solutions

The stability and surface evolution of solid-state nanopores in aqueous solutions are extremely important since they would get immersed in solutions during DNA translocation experiment for DNA analyses. In this work, we systematically studied the size evolution of SiN nanopores in ethanol, deionized water and potassium chloride (KCl) solutions by careful surface characterization and composition analyses using a transmission electron microscope. Surprisingly, we found that nanopores closed up completely in ethanol in an hour and showed a 30% and 20% size decrease in deionized water and KCl solutions, respectively. Strong evidence of surface oxidation was found by composition analyses in the nanopore area. Nanopore size evolution was strongly dependent on initial pore size and solution pH value. In pH = 13 KCl solution, SiN nanopores were observed to increase in size instead of decrease. The results not only provide useful information for DNA detection based on solid-state nanopores, but can also guide design and application of other nanodevices exposed to electrolyte-solvent systems such as cell-on-a-chip devices and biosensors.     

Molecular dynamics simulation on DNA translocating through MoS2 nanopores with various structures

The emergence of MoS₂ nanopores has provided a new avenue for high performance DNA sequencing, which is critical for modern chemical/biological research and applications. Herein, molecular dynamics simulations were performed to design a conceptual device to sequence DNA with MoS₂ nanopores of different structures (e.g., pore rim contained Mo atoms only, S atoms only, or both Mo and S atoms), where various unfolded single-stranded DNAs (ssDNAs) translocated through the nanopores driven by transmembrane bias; the sequence content was identified by the associating ionic current. All ssDNAs adsorbed onto the MoS₂ surface and translocated through the nanopores by transmembrane electric field in a stepwise manner, where the pause between two permeation events was long enough for the DNA fragments in the nanopore to produce well-defined ionic blockage current to deduce the DNA’s base sequence. The transmembrane bias and DNA-MoS₂ interaction could regulate the speed of the translocation process. Furthermore, the structure (atom constitution of the nanopore rim) of the nanopore considerably regulated both the translocate process and the ionic current. Thus, MoS₂ nanopores could be employed to sequence DNA with the flexibility to regulate the translocation process and ionic current to yield the optimal sequencing performance.     

PEG-Coated Large Mesoporous Silicas as Smart Platform for Protein Delivery and Their Use in a Collagen-Based Formulation for 3D Printing

Silica-based mesoporous systems have gained great interest in drug delivery applications due to their excellent biocompatibility and high loading capability. However, these materials face challenges in terms of pore-size limitations since they are characterized by nanopores ranging between 6–8 nm and thus unsuitable to host large molecular weight molecules such as proteins, enzymes and growth factors (GFs). In this work, for an application in the field of bone regeneration, large-pore mesoporous silicas (LPMSs) were developed to vehicle large biomolecules and release them under a pH stimulus. Considering bone remodeling, the proposed pH-triggered mechanism aims to mimic the release of GFs encased in the bone matrix due to bone resorption by osteoclasts (OCs) and the associated pH drop. To this aim, LPMSs were prepared by using 1,3,5-trimethyl benzene (TMB) as a swelling agent and the synthesis solution was hydrothermally treated and the influence of different process temperatures and durations on the resulting mesostructure was investigated. The synthesized particles exhibited a cage-like mesoporous structure with accessible pores of diameter up to 23 nm. LPMSs produced at 140 °C for 24 h showed the best compromise in terms of specific surface area, pores size and shape and hence, were selected for further experiments. Horseradish peroxidase (HRP) was used as model protein to evaluate the ability of the LPMSs to adsorb and release large biomolecules. After HRP-loading, LPMSs were coated with a pH-responsive polymer, poly(ethylene glycol) (PEG), allowing the release of the incorporated biomolecules in response to a pH decrease, in an attempt to mimic GFs release in bone under the acidic pH generated by the resorption activity of OCs. The reported results proved that PEG-coated carriers released HRP more quickly in an acidic environment, due to the protonation of PEG at low pH that catalyzes polymer hydrolysis reaction. Our findings indicate that LPMSs could be used as carriers to deliver large biomolecules and prove the effectiveness of PEG as pH-responsive coating. Finally, as proof of concept, a collagen-based suspension was obtained by incorporating PEG-coated LPMS carriers into a type I collagen matrix with the aim of designing a hybrid formulation for 3D-printing of bone scaffolds.     

Small‐Protein‐Stabilized Semiconductor Nanoprobe for Targeted Imaging of Cancer Cells

Recently, semiconductor nanoparticles such as quantum dots (QDs) have attracted significant attention for bioimaging. Complex chemical functionalization, surface modification, and bioconjugation chemistry are generally required to tag biomolecules to QDs for imaging of different biomarkers. In this study, we report a simple method for production of QDs stabilized by the small protein, Affibody (AF‐QDs) for fluorescent imaging of the human epidermal growth factor receptor type 2 (HER2) in human A549 lung cancer cells. This one‐pot synthesis of AF‐QDs avoids complex chemical conjugation procedures and demonstrates a promising approach for the preparation of fluorescent nanoprobes for imaging of cancer targets.     

Multivalent presentation of mannose on hyperbranched polyglycerol and their interaction with concanavalin A lectin

We describe the synthesis of multivalent mannose derivatives by using hyperbranched polyglycerols (hPG) as a scaffold with different linker structures. Grafting of protected mannose (Man) units is achieved by using Cu(I) -catalyzed Huisgen click chemistry with either an anomeric azide or propargyl ether onto complementarily functionalized alkyne or azido polymer surfaces. NMR spectroscopy, dynamic light scattering (DLS), IR spectroscopy, size-exclusion chromatography (SEC), and elemental analysis have been used to characterize the hPG-Man compounds. The surface availability and bioactivity of Man-modified polymers were evaluated by using a competitive surface plasmon resonance (SPR)-based binding assay by interactions of the glycopolymers with concanavalin A (Con A), a lectin that binds mannose containing molecules. The results indicated that the novel glycoarchitectures presented in this work are efficient inhibitors of Con A-mannose recognition and resulted in inhibitor concentrations (mean IC(50)) from the micro- to the nanomolar range, whereas the corresponding monovalent mannoside (methyl-Man) requires millimolar concentrations. The results provide an interesting structure-activity relationship for libraries of materials that differ in the linkage of the sugar moiety presented on a biocompatible polyglycerol scaffold.