Nanochannel Arrays Research Articles

Bulk heterojunction-induced ion transport in nanochannel arrays for light-enhanced osmotic energy conversion

A nanochannel array with ionic rectifying properties and excellent cation selectivity is presented. Under light irradiation, the bulk heterojunction-induced ionic current significantly increases the output power density.

Oriented Two‐Dimensional Covalent Organic Framework Membranes with High Ion Flux and Smart Gating Nanofluidic Transport

AbstractNanofluidic ion transport holds high promise in bio‐sensing and energy conversion applications. However, smart nanofluidic devices with high ion flux and modulable ion transport capabilities remain to be realised. Herein, we demonstrate smart nanofluidic devices based on oriented two‐dimensional covalent organic framework (2D COF) membranes with vertically aligned nanochannel arrays that achieved a 2–3 orders of magnitude higher ion flux compared with that of conventional single‐channel nanofluidic devices. The surface‐charge‐governed ion conductance is dominant for electrolyte concentration up to 0.01 M. Moreover, owing to the customisable pH‐responsivity of imine and phenol hydroxyl groups, the COF‐DT membranes attained an actively modulable ion transport with a high pH‐gating on/off ratio of ≈100. The customisable structure and rich chemistry of COF materials will offer a promising platform for manufacturing nanofluidic devices with modifiable ion/molecular transport features.

Oriented Two-Dimensional Covalent Organic Framework Membranes with High Ion Flux and Smart Gating Nanofluidic Transport.

Nanofluidic ion transport holds high promise in bio-sensing and energy conversion applications. However, smart nanofluidic devices with high ion flux and modulable ion transport capabilities remain to be realised. Herein, we demonstrate smart nanofluidic devices based on oriented two-dimensional covalent organic framework (2D COF) membranes with vertically aligned nanochannel arrays that achieved a 2-3 orders of magnitude higher ion flux compared with that of conventional single-channel nanofluidic devices. The surface-charge-governed ion conductance is dominant for electrolyte concentration up to 0.01 M. Moreover, owing to the customisable pH-responsivity of imine and phenol hydroxyl groups, the COF-DT membranes attained an actively modulable ion transport with a high pH-gating on/off ratio of ≈100. The customisable structure and rich chemistry of COF materials will offer a promising platform for manufacturing nanofluidic devices with modifiable ion/molecular transport features.

Designing asymmetrically modified nanochannel sensors using virtual EIS

Monitoring electrochemical impedance changes across an asymmetrically functionalized nanochannel array provides an attractive mechanism for chemical and biological sensors. Specific binding of the receptor molecules with their analyte leads to changes in charge distribution on the nanochannel surfaces modifying the ionic transport across them. The magnitude of impedance change due to receptor/ligand binding or sensor sensitivity depends on a large number of parameters and consequently, identification of parameters that result in sensitive and specific sensing performance is extremely tedious and cost-intensive. We rely on a ’virtual EIS’ procedure that models the transient ionic current due to a step-change in voltage to determine the frequency-dependent impedance of an asymmetrically functionalized nanochannel. This procedure is used to predict the impedance changes due to the specific binding of thrombin on nanochannel surfaces. Surface charge changes associated with the binding of thrombin protein on the aptamer coated surface result in a decrease of the membrane impedance and computational results suggest that a reduction in the ionic strength of the electrolyte leads to an increase in the magnitude of binding induced impedance reduction. Sensing experiments with thrombin binding aptamer are performed to evaluate the trends from the high-throughput computations. The agreement between model predictions and experimental observations suggests that the present modeling approach may be utilized to computationally evaluate sensor performance for a range of parameters and rapidly identify sensor configurations that enable point-of-care diagnostic devices with improved sensitivities.

Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale.

The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method’s basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method’s resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.

Self-doping of Nb2O5NC by cathodic polarization for enhanced conductivity properties and photoelectrocatalytic performance

A simple novel electrochemical reduction approach was developed for the self-doping of Nb4+ in niobium oxide nanochannels (Nb2O5NC), changing the conductivity, optical properties, and photocatalytic properties of the material. Nb2O5NC was synthesized using different electrolytes: 0.4 wt% HF in 1 M H2SO4 (EI), 0.4 M NH4F in glycerol (EII), and 0.25 g NH4F with 4 vol% water in glycol at 50 °C (EIII). Field emission scanning electron microscopy (FEG-SEM) analysis showed well-organized arrays of Nb2O5 nanochannels produced on Nb foil, with varying tube diameters in the order EII < EI < EIII and film thickness in the order EI < EII < EIII, which drastically affected the photocurrent vs. potential curves. In order to self-dope the Nb2O5, the samples were electrochemically reduced in 0.1 M KH2PO4 buffer solution (pH 10) for 5 min, at −2.5 V vs. Ag/AgCl, resulting in the doped samples denoted P-EI, P-EII, and P-EIII. The results showed that reduction of Nb5+ to Nb4+ occurred for all the Nb2O5NC samples, leading to decreased surface charge transfer resistance between the Nb2O5NC and the electrolyte, as well as increases of the charge carrier density and photocurrent for all the self-doped samples, compared to undoped samples. Sample P-EI was also tested for the degradation of reactive red 120 (RR120) dye, achieving efficient photoelectrocatalytic degradation of a 10 mg L−1 dye solution. These results reveal that the self-doping approach can enhance the photoelectrocatalytic properties of Nb2O5 photoanode, offering an alternative way for the removal of reactive dyes.

Revealing the Critical Role of Probe Grafting Density in Nanometric Confinement in Ionic Signal via an Experimental and Theoretical Study

The grafting density of probes at sensor interface plays a critical role in the performance of biochemical sensors. However, compared with macroscopic interface, the effects of probe grafting density at nanometric confinement are rarely studied due to the limitation of precise grafting density regulation and characterization at the nanoscale. Here, we investigate the effect from the grafting density of DNA probes on ionic signal for nucleic acid detection in a cylindrical nanochannel array (with diameter of 25 nm) by combing experiments and theories. We set up a theoretical model of charge distribution from close to inner wall of nanochannels at low probe grafting density to spreading in whole space at high probe grafting density. The theoretical results fit well with the experimental results. A reverse of ionic output from signal-off to signal-on occurs with increasing probe grafting density. Low probe grafting density offers a high current change ratio that is further enhanced using long-chain DNA probes or the electrolyte with a low salt concentration. This work develops an approach to enhance performance of nanochannel-based sensors and explore physicochemical properties in nanometric confines.

Single-molecule telomere length characterization by optical mapping in nano-channel array: Perspective and review on telomere length measurement

In humans, the telomere consists of tandem 5′TTAGGG3′ DNA repeats on both ends of all 46 chromosomes. Telomere shortening has been linked to aging and age-related diseases. Similarly, telomere length changes have been associated with chemical exposure, molecular-level DNA damage, and tumor development. Telomere elongation has been associated to tumor development, caused due to chemical exposure and molecular-level DNA damage. The methods used to study these effects mostly rely on average telomere length as a biomarker. The mechanisms regulating subtelomere-specific and haplotype-specific telomere lengths in humans remain understudied and poorly understood, primarily because of technical limitations in obtaining these data for all chromosomes. Recent studies have shown that it is the short telomeres that are crucial in preserving chromosome stability. The identity and frequency of specific critically short telomeres potentially is a useful biomarker for studying aging, age-related diseases, and cancer. Here, we will briefly review the role of telomere length, its measurement, and our recent single-molecule telomere length measurement assay. With this assay, one can measure individual telomere lengths as well as identify their physically linked subtelomeric DNA. This assay can also positively detect telomere loss, characterize novel subtelomeric variants, haplotypes, and previously uncharacterized recombined subtelomeres. We will also discuss its applications in aging cells and cancer cells, highlighting the utility of the single molecule telomere length assay.

Capillary trapping induced slow evaporation in nanochannels

Unconventional reservoirs are massive and providing an increasing share of global energy with a broad group of stakeholders in academia, industry and government. The size of pores in unconventional reservoirs can be down to nanometers, necessitating a deeper fundamental understanding of fluid phase properties at nanoscale. In this paper, we investigate capillary trapping induced slow evaporation of n-pentane in nanochannel arrays through isothermal pressure drawdown to mimic the hydrocarbon release in nanopores of low-permeability reservoirs. Importantly, the capillary trapping forms during a slow reservoir pressure reduction process and significantly impedes liquid evaporation. Compared to the evaporation case without any capillary trapping, the global evaporation rate is ~16 times lower, which unfavorably affects gas recovery. In addition, we observe liquid corner flow in assisting evaporation in nanochannel, providing important experimental evidence towards previous theoretical study. In brief, our work reveals a type of anomalous evaporation at nanoscale that is fundamentally relevant to shale gas recovery. The experimental and modeling finding indicates that regulating pressure drawdown at an appropriate rate plays a key role in efficiently extracting shale gas.

Internal Motion of Chromatin Fibers Is Governed by Dynamics of Uncompressed Linker Strands

Chromatin compaction and internal motion are fundamental aspects of gene expression regulation. Here, we have investigated chromatin fibers comprising recombinant histone octamers reconstituted with double-stranded bacteriophage T4-DNA. The size of the fibers approaches the typical size of genomic topologically associated domains. Atomic force and fluorescence (correlation) microscopy have been used to assess the structural organization, histone-induced compaction, and internal motion. In particular, the fibers are stretched on arrays of nanochannels, each channel with a diameter of 60 or 125 nm. Major intrafiber segregation and fast internal fluctuations are observed. Full compaction was only achieved by triggering an attractive nucleosome interaction through the addition of magnesium cations. Besides compaction, histone complexation results in a dramatic decrease in the fiber’s relaxation time. The relaxation times are similar to those of naked DNA with a comparable stretch, which indicates that internal motion is governed by the dynamics of uncompressed linker strands. Furthermore, the main reorganization process is association-dissociation of individually compacted regions. We surmise that the modulation of chromatin’s internal motion by histone complexation might have implications for transcriptional bursting.

Abstract 4897: Genome-wide structural variation analysis and characterization of Hepatitis B Virus integration sites in hepatocellular carcinomas using Bionano Genomics whole genome imaging

Abstract Large genomic rearrangements are known contributors to cancer formation. Hepatitis B virus (HBV) integration is a frequent driver of hepatocellular carcinoma, frequently associated with genomic rearrangements. Next generation sequencing (NGS) is commonly used to study these integration sites and rearrangements; however, due to short read lengths, NGS is often unable to characterize large and complicated genomic rearrangements. To solve this problem, whole genome imaging was used to perform genome-wide detection of large structural variants (SVs) in DNA extracted from liver tumors, including characterization of HBV viral integration sites and nearby rearrangements. Ultra-high molecular weight DNA was extracted from liver tissue of four patients diagnosed with hepatocellular carcinoma. The DNA was fluorescently labeled at the motif CTTAAG, linearized, and imaged in nanochannel arrays using a Bionano Genomics Saphyr platform. Images of molecules were converted into digital single-molecule reads. 400X coverage of DNA molecules at least 150 kbp in length was collected for each sample. For three of the patients, somatic structural variants (SV) were identified by comparing SV calls and single molecule DNA reads of liver tumor resections against those of matching physiologically normal liver tissue. For the fourth patient, putative somatic SVs were identified by comparing SV calls against a database of 59,490 known variants from 57 physiologically normal individuals. Among the matched-pair samples, 511 large tumor-unique structural variants were identified. For the fourth sample, 619 putative somatic events were identified. HBV viral integration sites, which had previously been identified via NGS, and nearby SVs were characterized. Complex SVs were resolved, including translocation events with several loci. These findings demonstrate the utility of whole genome imaging for studying the relationship between viral integration and cancer. Citation Format: Karl Hong, Camille Péneau, Quentin Bayard, Sandrine Imbeaud, Andy Pang, Alex Hastie, Eric Letouzé, Jessica Zucman-Rossi. Genome-wide structural variation analysis and characterization of Hepatitis B Virus integration sites in hepatocellular carcinomas using Bionano Genomics whole genome imaging [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4897.

Ionic Current Rectification Triggered Photoelectrochemical Chiral Sensing Platform for Recognition of Amino Acid Enantiomers on Self-Standing Nanochannel Arrays.

Chirality is an intrinsic and essential property of nature, and the enantiomeric discrimination of chiral molecules can provide important information leading to a better understanding of chiral recognition in biological systems and furthering the development of useful molecular devices in biochemical and pharmaceutical studies. Therefore, the exploration of new detection techniques with high accuracy and reliability for high-throughput enantioselective detection is still highly desirable. Herein, a chiral enantiomers selective recognition platform based on self-standing titanium dioxide nanochannel arrays (TiO2 NCAs) is proposed to implement the ionic current rectification triggered photoelectrochemical (PEC) detection, which provides a novel sensing platform to discriminate chiral amino acid through synchronous output dual response signals of ionic current and photocurrent. The utilization of nanochannel arrays guaranteed the high-throughput detection, and the dual signal model avoided a "false positive" detection. In addition, based on the fabricated detection platform, various chiral substances can be facilely detected through integrating different chiral regulation units, which shed light on the construction of reliable chiral sensors for practical applications in a biological environment.

Ion transmission through nanochannels: Energy dependent acceptance angle and transmission probability

The transmission of energetic (0.1–2 MeV) light ions through an array of parallel nanochannels was measured as a function of incident angle with respect to the channel axis. The angular transmission can be viewed macroscopically, similar to an ion passing through a collection of parallel slits which then determine the beam profile or similar to ion channeling in crystals. In the first case, the number of transmitted ions as a function of incident angle would be determined simply by the line-of-sight geometry (length over diameter) of the nanotube resulting in a critical angle of about 0.2° whereas in the second case, the acceptance angle would be much larger, nearly 0.8°, and analogous to the acceptance angle typically encountered in ion channeling in crystals. The measured critical angle varies between 0.4° and 0.8° depending on the incident ion energy, but with increasing energy the critical angle becomes larger rather than smaller. The transmittance at the optimal angle increases with energy and shows a strong linear correlation with it. This can be understood as a consequence of repeated interactions with the channel walls as the channeled ions travel along the channel.

Electrochemical preparation of Nb2O5 nanochannel photoelectrodes for enhanced photoelectrocatalytic performance in removal of RR120 dye

The present work describes the synthesis of niobium oxide nanochannels (Nb2O5NCs) with high surface area, porosity, photocurrent density, and photoelectrochemical stability as photocatalyst. The Nb2O5NCs were prepared by electrochemical anodization of niobium foil in different electrolytes: 1 M H2SO4 containing 0.4 wt% HF (S1); glycerol containing 0.4 M NH4F (S2); 0.25 g NH4F with 4 vol% water in glycol at 50 °C (S3); and glycerol containing 10 wt% K2HPO4, at 130 °C (S4, annealed in air; S5, annealed in N2). All the Nb2O5NCs showed well-organized arrays of nanochannels grown on the Nb foil, with tube diameters in the order S4<S2<S1<S3 and film thicknesses in the order S1<S2<S3<S4, as determined using FEG-SEM analyses. The samples were also characterized using XRD, EDX, DRS, XPS, EIS, Mott-Schottky analysis, and LSV curves. But, best results were obtained only when phosphorus (about 1% doping) was incorporated into the electrodes samples prepared in glycerol containing 10 wt% K2HPO4 at 130 °C (i.e. S4 and S5). This procedure enhances the absorption intensity in the UV–Vis regions, the conductivity, the charge carrier density, and the photocurrent density. The Nb2O5NC sample S5 was tested for the degradation of Procion Red HE-3B (RR120) dye, as a model pollutant, achieving efficient photoelectrodegradation with nearly 2 times higher mineralization efficiency compared to photolysis (PT) and photocatalysis (PC). Thus, the results indicate that the modification of Nb2O5NC thin film photoelectrodes by phosphorous doping can be a powerful and efficient alternative to usual approaches applied to the treatment of complex reactive dyes.

Fin-Gated Nanochannel Array Gate-Recessed AlGaN/GaN Metal-Oxide-Semiconductor High-Electron-Mobility Transistors

In this article, fin-gated nanochannel array gate-recessed AlGaN/GaN metal-oxide-semiconductor high-electron-mobility transistors (MOSHEMTs) were fabricated, in which the gate oxide layer was directly grown using the photoelectrochemical (PEC) oxidation method, the gate-recessed structure was formed using the PEC etching method, and the nanochannel array was patterned using the electron-beam lithography system. The improved gate controllability was obtained in devices with a narrower channel width due to the lateral field effect in comparison with those of the conventional planar AlGaN/GaN MOSHEMTs. A threshold voltage of −0.30, −0.35, and −2.3 V, and a subthreshold swing of 95, 109, and 372 mV/dec, were respectively obtained for the AlGaN/GaN MOSHEMTs with a channel width of 80 and 100 nm, and with a planar channel. Furthermore, the associated extrinsic transconductance of 269, 253, and 93 mS/mm was obtained to verify the improved performance of AlGaN/GaN MOSHEMTs using a narrower channel array. Besides, the low-noise and high-frequency performances were also enhanced using a narrower channel width in the fin-gated nanochannel array gate-recessed AlGaN/GaN MOSHEMTs.

Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping.

Detailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, we use high throughput optical mapping of large single DNA molecules in nanochannel arrays for 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes and determine the frequencies and contexts of specific subtelomeric duplicons on each chromosome arm, helping to clarify the currently ambiguous nature of many specific subtelomere structures as represented in the current reference sequence (HG38). The organization and content of some duplicons in subtelomeres appear to show both chromosome arm and population-specific trends. Based upon these trends we estimate a timeline for the spread of these duplication blocks.

Nanoporous AlSBA-15 catalysed Claisen–Schmidt condensation for the synthesis of novel and biologically active chalcones

Mesoporous AlSBA-15 catalysts (nSi/nAl ratios of 41, 129 and 210) were synthesized by sol–gel method. These materials were characterized by XRD, N2 sorption, FTIR, TPD-NH3, FESEM, EDX, and TEM analysis. XRD analysis of AlSBA-15 catalysts confirmed the existence of well-ordered crystalline structure having p6mm symmetry. N2 sorption isotherm of AlSBA-15 catalysts showed a type IV adsorption isotherm with H1 hysteresis loops. SEM analysis of AlSBA-15 (41) indicated worm-like particle morphology with a size range of 3 μm with co-occurrence of smaller particles of size ca. 1 μm. TEM analysis of AlSBA-15 (41) showed existence of uniform array of tubular nano-channels. The catalytic application of AlSBA-15 catalysts was tested on industrially important chalcones synthesis via Claisen–Schmidt condensation reaction in environment friendly approach. The reaction parameters such as time, temperature, nSi/nAl ratio, catalyst amount, and catalyst stability were investigated. AlSBA-15 (41) catalyst showed an excellent catalytic performance with 98% 1-tetralone conversion with 100% selectivity of compound 1c (91% yield) within 120 min AlSBA-15 (129) and AlSBA-15 (210) catalysts. The anti-oxidant activity of the synthesised chalcones were investigated by various in-vitro procedures, including radical scavenging potentials-1, 1-diphenyl-2-picryl-hydrazil, hydrogen peroxide scavenging, and ferric reducing potential assay. The new chalcone derivatives synthesised in this work showed a very good antioxidant activity and some were found to be more active than the parent chalcones, (E)-3-(4-hydroxy-3-methoxyphenyl)-1-phenylprop-2-en-1-one (compound 8c), and standard antioxidant (curcumin).

Cover: Journal of the Chinese Chemical Society 1/2020

In this paper, anodic aluminum oxide films form globally self‐aligned and locally self‐organized order nanochannels with characteristic diameter/spacing and unmatched aspect ratio. The range of order can be increased tremendously by various lithographic guiding methods. Focused ion beam can selectively close individual nanochannels to fabricate arrays with custom‐designed geometry, which can be exploited to create arrays of nanochannels with different diameters after subsequent chemical etching. By controlling the anodization voltage to change the characteristic diameter/spacing, nanochannles can be bended and enlarged to change their longitudinal geometry, forming arrays with fascinating 3‐dimensional architecture. More details about this figure will be discussed by Prof. Yuh‐Lin Wang and his co‐workers on page 11~24 in this issue. image

Controlling the alignment of 1D nanochannel arrays in oriented metal-organic framework films for host-guest materials design.

Controlling the direction of molecular-scale pores enables the accommodation of guest molecular-scale species with alignment in the desired direction, allowing for the development of high-performance mechanical, thermal, electronic, photonic and biomedical organic devices (host–guest approach). Regularly ordered 1D nanochannels of metal–organic frameworks (MOFs) have been demonstrated as superior hosts for aligning functional molecules and polymers. However, controlling the orientation of MOF films with 1D nanochannels at commercially relevant scales remains a significant challenge. Here, we report the fabrication of macroscopically oriented films of Cu-based pillar-layered MOFs having regularly ordered 1D nanochannels. The direction of 1D nanochannels is controllable by optimizing the crystal growth process; 1D nanochannels align either perpendicular or parallel to substrates, offering molecular-scale pore arrays for a macroscopic alignment of functional guest molecules in the desired direction. Due to the fundamental interest and widespread technological importance of controlling the alignment of functional molecules and polymers in a particular direction, orientation-controllable MOF films will open up the possibility of realising the potential of MOFs in advanced technologies.

Creating anodic alumina nanochannel arrays with custom‐made geometry

AbstractPorous anodic alumina oxide (AAO) is one of the most commonly used nanotemplates for growing arrays of nanoparticles, nanowires, nanocomposites, and nanoarchitectures because its pores, which are of a very uniform size, can grow longitudinally into arrays of self‐aligned nanochannels with an extremely high aspect ratio. Furthermore, under specific combinations of anodization voltage and electrolyte, the lateral positions of nanochannels can self‐organize into arrays of two‐dimensional hexagonally close‐packed lattices with domain sizes on the order of few tens of lattice units. The domain size can be greatly increased by prepatterning the Al surface with custom‐designed nanoconcaves prior to the anodization process. The concaves guide the growth fronts of nanochannels and lead to the formation of an ideally long‐range ordered lattice of nanochannel array. Such concaves have been fabricated by many methods, such as stamp imprinting, grating imprinting, and focused ion beam direct writing. In this review, we summarize the development of various methods to create AAO nanochannel arrays with custom‐made geometry and discuss the mechanism responsible for the guiding process.