DNA base detection using a single-layer MoS2

Machine learning empowered next generation DNA sequencing: perspective and prospectus

The pursuit of ultra-rapid, cost-effective, and accurate DNA sequencing is a highly sought after aspect of personalized medicine development. With recent advancements, mainstream machine learning (ML) algorithms hold immense promise for high throughput DNA sequencing at the single nucleotide level. While ML has revolutionized multiple domains of nanoscience and nanotechnology, its implementation in DNA sequencing is still in its preliminary stages. ML-aided DNA sequencing is especially appealing, as ML has the potential to decipher complex patterns and extract knowledge from complex datasets. Herein, we present a holistic framework of ML-aided next-generation DNA sequencing with domain knowledge to set directions toward the development of artificially intelligent DNA sequencers. This perspective focuses on the current state-of-the-art ML-aided DNA sequencing, exploring the opportunities as well as the future challenges in this field. In addition, we provide our personal viewpoints on the critical issues that require attention in the context of ML-aided DNA sequencing.

Effect of Membrane Thickness on Ion Transport in pH-Regulated Zero-Depth Interfacial Nanopores

Zero-depth interfacial nanopores, which are formed by two crossed nanoscale channels at their intersection interface, have been proposed to increase the spatial resolution of solid-state nanopores. However, research on zero-depth interfacial nanopores is still in its early stages. Although it has been shown that the current passing through an interfacial nanopore is largely independent of the membrane thickness, existing studies have not fully considered the impact of membrane thickness on other ion transport characteristics within these nanopores. In this paper, we investigate the electrokinetic ion transport phenomenon in the zero-depth interfacial nanopores, especially focusing on the influence of membrane thickness on the ion transport phenomenon. Our model incorporates the Poisson-Nernst-Planck equations and the Navier-Stokes equations, featuring a pH-regulated surface charge density. We find that when the thickness of the nanochannels is close to the interface size of the formed interfacial nanopore, the phenomenon of ion transport in the interfacial nanopore is similar to that in a conventional cylindrical nanopore. However, when the thickness of the nanochannels is much greater than the interface size of the formed interfacial nanopore, several distinct phenomena occur. The surface charge density on the inner walls of the interfacial nanopores has a small peak at the interface of the two crossing nanochannels, and the anion concentration changes greatly between the two nanochannels; that is, a much greater anion concentration forms in the nanochannel near the anode side than in the nanochannel near the cathode side. When the surface charge is nonzero, the electric field within the interfacial nanopore creates three extreme points, and the directions of the local electric fields are opposite at the ends of the membrane.

Observation of Ultrahigh Photoconductivity in DNA-MoS2 Nano-Biocomposite

A nano-biocomposite film with ultrahigh photoconductivity remains elusive and critical for bio-optoelectronic applications. A uniform, well-connected, high-concentration nanomaterial network in the biological matrix remains challenging to achieve high photoconductivity. Wafer-scale continuous nano-biocomposite film without surface deformations and cracks plays another major obstacle. Here ultrahigh photoconductivity is observed in deoxyribonucleic acid-molybdenum disulfide (DNA-MoS2) nano-biocomposite film by incorporating a high-concentration, well-percolated, and uniform MoS2 network in the ss-DNA matrix. This is achieved by utilizing DNA-MoS2 hydrogel formation, which results in crack-free, wafer-scale DNA-MoS2 nano-biocomposite films. Ultra-high photocurrent (5.5 mA at 1 V) with a record-high on/off ratio (1.3 × 106) is observed, five orders of magnitude higher than conventional biomaterials (≈101) reported so far. The incorporation of the Wely semimetal (Bismuth) as an electrical contact exhibits ultrahigh photoresponsivity (2.6 × 105 A W-1). Such high photoconductivity in DNA-MoS2 nano-biocomposite could bridge the gap between biology, electronics, and optics for innovative biomedicine, bioengineering, and neuroscience applications.

Detecting Hachimoji DNA: An Eight-Building-Block Genetic System with MoS2 and Janus MoSSe Monolayers

In the pursuit of personalized medicine, the development of efficient, cost-effective, and reliable DNA sequencing technology is crucial. Nanotechnology, particularly the exploration of two-dimensional materials, has opened different avenues for DNA nucleobase detection, owing to their impressive surface-to-volume ratio. This study employs density functional theory with van der Waals corrections to methodically scrutinize the adsorption behavior and electronic band structure properties of a DNA system composed of eight hachimoji nucleotide letters adsorbed on both MoS2 and MoSSe monolayers. Through a comprehensive conformational search, we pinpoint the most favorable adsorption sites, quantifying their adsorption energies and charge transfer properties. The analysis of electronic band structure unveils the emergence of flat bands in close proximity to the Fermi level post-adsorption, a departure from the pristine MoS2 and MoSSe monolayers. Furthermore, leveraging the nonequilibrium Green's function approach, we compute the current-voltage characteristics, providing valuable insights into the electronic transport properties of the system. All hachimoji bases exhibit physisorption with a horizontal orientation on both monolayers. Notably, base G demonstrates high sensitivity on both substrates. The obtained current-voltage (I-V) characteristics, both without and with base adsorption on MoS2 and the Se side of MoSSe, affirm excellent sensing performance. This research significantly advances our understanding of potential DNA sensing platforms and their electronic characteristics, thereby propelling the endeavor for personalized medicine through enhanced DNA sequencing technologies.

Effect of surface functionalization on DNA sequencing using MXene-based nanopores

As one of the most promising types of label-free nanopores has great potential for DNA sequencing via fast detection of different DNA bases. As one of the most promising types of label-free nanopores, two-dimensional nanopore materials have been developed over the past two decades. However, how to detect different DNA bases efficiently and accurately is still a challenging problem. In the present work, the translocation of four homogeneous DNA strands (i.e., poly(A)20, poly(C)20, poly(G)20, and poly(T)20) through two-dimensional transition-metal carbide (MXene) membrane nanopores with different surface terminal groups is investigated via all-atom molecular dynamics simulations. Interestingly, it is found that the four types of bases can be distinguished by different ion currents and dwell times when they are transported through the Ti3C2(OH)2 nanopore. This is mainly attributed to the different orientation and position distributions of the bases, the hydrogen bonding inside the MXene nanopore, and the interaction of the ssDNA with the nanopore. The present study enhances the understanding of the interaction between DNA strands and MXene nanopores with different functional groups, which may provide useful guidelines for the design of MXene-based devices for DNA sequencing in the future.

Influence of nanopore coating patterns on the translocation dynamics of polyelectrolytes

Polyelectrolytes can electrophoretically be driven through nanopores in order to be detected. The respective translocation events are often very fast and the process needs to be controlled to promote efficient detection. To this end, we attempt to control the translocation dynamics by coating the inner surface of a nanopore. For this, different charge distributions are chosen that result in substantial variations of the pore-polymer interactions. In addition and in view of the existing detection modalities, experimental settings, and nanopore materials, different types of sensors inside the nanopore have been considered to probe the translocation process and its temporal spread. The respective transport of polyelectrolytes through the coated nanopores is modeled through a multi-physics computational scheme that incorporates a mesoscopic/electrokinetic description for the solvent and particle-based scheme for the polymer. This investigation could underline the interplay between sensing modality, nanopore material, and detection accuracy. The electro-osmotic flow and electrophoretic motion in a pore are analyzed together with the polymeric temporal and spatial fluctuations unraveling their correlations and pathways to optimize the translocation speed and dynamics. Accordingly, this work sketches pathways in order to tune the pore-polymer interactions in order to control the translocation dynamics and, in the long run, errors in their measurements.

Adsorption of DNA nucleobases on single-layer Ti3C2 MXene and graphene: vdW-corrected DFT and NEGF studies

We investigated the interaction of DNA nucleobases [adenine (A), guanine (G), thymine (T), and cytosine (C)] with single-layer Ti3C2 MXene using Van der Waals (vdW)-corrected density functional theory and non-equilibrium Green's function methods. All calculations were benchmarked against graphene. We showed that depending on the initial vertical height of a nucleobase above the Ti3C2 surface, two interaction mechanisms are possible, namely, physisorption and chemisorption. For graphene, DNA nucleobases always physisorbed onto the graphene surface irrespective of the initial vertical height of the nucleobase above the graphene sheet. The PBE+vdW binding energies for graphene are high (0.55-0.74 eV) and follow the order G > A > T > C, with adsorption heights in the range of 3.16-3.22 Å, indicating strong physisorption. For Ti3C2, the PBE+vdW binding energies are relatively weaker (0.16-0.20 eV) and follow the order A > G = T > C, with adsorption heights in the range of 5.51-5.60 Å, indicating weak physisorption. The binding energies for chemisorption follow the order G > A > T > C, which is the same order for physisorption. The binding energy values (5.3-7.5 eV) indicate very strong chemisorption (∼40 times larger than the physisorption binding energies). Furthermore, our band structure and electronic transport analysis showed that for physisorption, there is neither significant variation in the band structure nor modulation in the transmission function and device density of states. The relatively weak physisorption and strong chemisorption show that Ti3C2 might not be capable of identifying DNA nucleobases using the physisorption method.

Dwell Time Prolongation and Identification of Single Nucleotides Passing through a Solid-State Nanopore by Using Ammonium Sulfate Aqueous Solution

The ionic current blockades when poly(dT)₆₀ or dNTPs passed through SiN nanopores in an aqueous solution containing (NH₄)₂SO₄ were investigated. The dwell time of poly(dT)₆₀ in the nanopores in an aqueous solution containing (NH₄)₂SO₄ was significantly longer compared to that in an aqueous solution that did not contain (NH₄)₂SO₄. This dwell time prolongation effect due to the aqueous solution containing (NH₄)₂SO₄ was also confirmed when dCTP passed through the nanopores. In addition, when the nanopores were fabricated via dielectric breakdown in the aqueous solution containing (NH₄)₂SO₄, the dwell time prolongation effect for dCTP still occurred even after the aqueous solution was displaced with the aqueous solution without (NH₄)₂SO₄. Furthermore, we measured the ionic current blockades when the four types of dNTPs passed through the same nanopore, and the four types of dNTPs could be statistically identified according to their current blockade values.

Two Detection Modes of Nanoslit Sensing Based on Planar Heterostructure of Graphene/Hexagonal Boron Nitride

Solid-state nanopore sequencing is now confronted with problems of stochastic pore clogging and too fast speed during the DNA permeation through a nanopore, although this technique is revolutionary with long readability and high efficiency. These two problems are related to controlling molecular transportation during sequencing. To control the DNA motion and identify the four bases, we propose nanoslit sensing based on the planar heterostructure of two-dimensional graphene and hexagonal boron nitride. Molecular dynamics simulations are performed on investigating the motion of DNA molecules on the heterostructure with a nanoslit sensor. Results show that the DNA molecules are confined within the hexagonal boron nitride (HBN) domain of the heterostructure. And the confinement effects of the heterostructure can be optimized by tailoring the stripe length. Besides, there are two ways of DNA permeation through nanoslits: the DNA can cross or translocate the nanoslit under applied voltages along the y and z directions. The two detection modes are named cross-slit and trans-slit, respectively. In both modes, the ionic current drops can be observed when the nanoslit is occupied by the DNA. And the ionic currents and dwell times can be simultaneously detected to identify the four different DNA bases. This study can shed light on the sensing mechanism based on the nanoslit sensor of a planar heterostructure and provide theoretical guidance on designing devices controlling molecular transportation during nanopore sequencing.

High durability and stability of 2D nanofluidic devices for long-term single-molecule sensing

Nanopores in two-dimensional (2D) membranes hold immense potential in single-molecule sensing, osmotic power generation, and information storage. Recent advances in 2D nanopores, especially on single-layer MoS2, focus on the scalable growth and manufacturing of nanopore devices. However, there still remains a bottleneck in controlling the nanopore stability in atomically thin membranes. Here, we evaluate the major factors responsible for the instability of the monolayer MoS2 nanopores. We identify chemical oxidation and delamination of monolayers from their underlying substrates as the major reasons for the instability of MoS2 nanopores. Surface modification of the substrate and reducing the oxygen from the measurement solution improves nanopore stability and dramatically increases their shelf-life. Understanding nanopore growth and stability can provide insights into controlling the pore size, shape and can enable long-term measurements with a high signal-to-noise ratio and engineering durable nanopore devices.

Solid-State Nanopore Array: Manufacturing and Applications

Nanopore brings extraordinary properties for a variety of potential applications in various industrial sectors. Since manufacturing of solid-state nanopore is first reported in 2001, solid-state nanopore has become a hot topic in the recent years. An increasing number of manufacturing methods have been reported, with continuously decreased sizes from hundreds of nanometers at the beginning to ≈1 nm until recently. To enable more robust, sensitive, and reliable devices required by the industry, researchers have started to explore the possible methods to manufacture nanopore array which presents unprecedented challenges on the fabrication efficiency, accuracy and repeatability, applicable materials, and cost. As a result, the exploration of fabrication of nanopore array is still in the fledging period with various bottlenecks. In this article, a wide range of methods of manufacturing nanopores are summarized along with their achievable morphologies, sizes, inner structures for characterizing the main features, based on which the manufacturing of nanopore array is further addressed. To give a more specific idea on the potential applications of nanopore array, some representative practices are introduced such as DNA/RNA sequencing, energy conversion and storage, water desalination, nanosensors, nanoreactors, and dialysis.

High-Figure-of-Merit Biosensing and Enhanced Excitonic Absorption in an MoS2-Integrated Dielectric Metasurface

Among the transitional metal dichalcogenides (TMDCs), molybdenum disulfide (MoS₂) is considered an outstanding candidate for biosensing applications due to its high absorptivity and amenability to ionic current measurements. Dielectric metasurfaces have also emerged as a powerful platform for novel optical biosensing due to their low optical losses and strong near-field enhancements. Once functionalized with TMDCs, dielectric metasurfaces can also provide strong photon-exciton interactions. Here, we theoretically integrated a single layer of MoS₂ into a CMOS-compatible asymmetric dielectric metasurface composed of TiO₂ meta-atoms with a broken in-plane inversion symmetry on an SiO₂ substrate. We numerically show that the designed MoS₂-integrated metasurface can function as a high-figure-of-merit (FoM=137.5 RIU-1) van der Waals-based biosensor due to the support of quasi-bound states in the continuum. Moreover, owing to the critical coupling of the magnetic dipole resonances of the metasurface and the A exciton of the single layer of MoS₂, one can achieve a 55% enhanced excitonic absorption by this two-port system. Therefore, the proposed design can function as an effective biosensor and is also practical for enhanced excitonic absorption and emission applications.

Ab Initio Molecular Dynamics Simulation of Water Transport through Short Carbon Nanotubes

Water transport through short single-walled (6, 6) carbon nanotubes (CNTs) was investigated with ab initio molecular dynamics (AIMD) simulation at different temperatures. The water molecules under extreme confinement present a one-dimensional jagged pattern owing to hydrogen bonding, with the near-perfect alignment of the dipole orientations. CNTs ending with dangling bonds can promote water dissociation near the entrance and the occurrence of dipole flipping along the water wire at high temperatures, accompanied by the formation of D defects and L defects in the hydrogen-bond network. In contrast, dissociation of water molecules rarely takes place if the dangling bonds at the ends of the CNTs are terminated with H atoms. Angular jumps of water molecules are commonplace inside the narrow CNTs, implying a low-energy barrier for hydrogen-bond exchange among water molecules in narrow CNTs. The simulation results demonstrate the high activity of dangling bonds at the ends of short CNTs, accompanying passivation processes and their profound impact on water structure and transport, which is important for diverse technological applications.

Which 2D Material is Better for DNA Detection: Graphene, MoS2, or MXene?

Despite much research on characterizing 2D materials for DNA detection with nanopore technology, a thorough comparison between the performance of different 2D materials is currently lacking. In this work, using extensive molecular dynamics simulations, we compare nanoporous graphene, MoS₂ and titanium carbide MXene (Ti₃C₂) for their DNA detection performance and sensitivity. The ionic current and residence time of DNA are characterized in each nanoporous materials by performing hundreds of simulations. We devised two statistical measures including the Kolmogorov-Smirnov test and the absolute pairwise difference to compare the performance of nanopores. We found that graphene nanopore is the most sensitive membrane for distinguishing DNA bases. The MoS₂ is capable of distinguishing the A and T bases from the C and G bases better than graphene and MXene. Physisorption and the orientation of DNA in nanopores are further investigated to provide molecular insight into the performance characteristics of different nanopores.

Edges in bilayered h-BN: insights into the atomic structure

This study is devoted to the study of the edges of bilayered h-BN, whose atomic structure was previously generally unknown. It is shown that the edges tend to connect regardless of the edge cut. A defectless connection can be expected only in the case of a zigzag edge, while in other cases a series of tetragonal and octagonal defects will be formed. This result was obtained by carrying out an analogy between the edge of bilayered h-BN and the interface of monolayer h-BN. Information on the structure and energetics of closed edges allowed us to predict the shape of holes in h-BN, which agreed with the reference experimental data. Finally, it is shown that the closed edges do not create electronic states in the band gap, thus not changing the dielectricity of h-BN.

Ionic Liquid Decelerates Single-Stranded DNA Transport through Molybdenum Disulfide Nanopores

Nanopores in two-dimensional (2D) materials have emerged to offer in principle necessary spatial resolution for high-throughput DNA sequencing. However, their fidelity is severely limited by the fast DNA translocation. A recent experiment indicates that introducing ionic liquids could slow down DNA translocation in a MoS₂ nanopore. However, the corresponding in-depth molecular mechanism underlying the experimental findings is not fully understood, which is crucial for the future improvement of rational DNA translocation control. Here, we computationally investigate and then experimentally identify the effect of BmimCl ionic liquid on the retardation of ssDNA translocation through a single-layer MoS₂ nanopore. Our all-atom molecular dynamics simulations demonstrate that the strong interaction between Bmim⁺ and ssDNA offers a considerable dragging force to decelerate the electrophoretic motion of ssDNA in the BmimCl solution. Moreover, we show that Bmim⁺ ions exhibit preferential binding on the sulfur edges of the nanopore. These Bmim⁺ in the pore region can not only act as a steric blockage but also form π-π stackings with nucleobases, which provide a further restriction on the ssDNA motion. Therefore, our molecular dynamics simulation investigations deepen the understanding of the critical role of ionic liquid in DNA translocation through a nanopore from a molecular landscape, which may benefit practical implementations of ionic liquids in nanopore sequencing.

Discriminating protein tags on a dsDNA construct using a Dual Nanopore Device

We report Brownian dynamics simulation results with the specific goal to identify key parameters controlling the experimentally measurable characteristics of protein tags on a dsDNA construct translocating through a double nanopore setup. First, we validate the simulation scheme in silico by reproducing and explaining the physical origin of the asymmetric experimental dwell time distributions of the oligonucleotide flap markers on a 48 kbp long dsDNA at the left and the right pore. We study the effect of the electric field inside and beyond the pores, critical to discriminate the protein tags based on their effective charges and masses revealed through a generic power-law dependence of the average dwell time at each pore. The simulation protocols monitor piecewise dynamics at a sub-nanometer length scale and explain the disparate velocity using the concepts of nonequilibrium tension propagation theory. We further justify the model and the chosen simulation parameters by calculating the Péclet number which is in close agreement with the experiment. We demonstrate that our carefully chosen simulation strategies can serve as a powerful tool to discriminate different types of neutral and charged tags of different origins on a dsDNA construct in terms of their physical characteristics and can provide insights to increase both the efficiency and accuracy of an experimental dual-nanopore setup.

On the interface between biomaterials and two-dimensional materials for biomedical applications

Two-dimensional (2D) materials have garnered significant attention due to their ultrathin 2D structures with a high degree of anisotropy and functionality. Reliable manipulation of interfaces between 2D materials and biomaterials is a new frontier for biomedical nanoscience and combining biomaterials with 2D materials offers a promising way to fabricate innovative 2D biomaterials composites with distinct functionality for biomedical applications. Here, we focus exclusively on a summary of the current work in the interface investigation of 2D biomaterials. Specifically, we highlight extraordinary features that make 2D materials so desirable, as well as the molecular level interactions between 2D materials and biomaterials that have been studied thus far. Furthermore, the approaches for investigating the interface characteristics of 2D biomaterials are presented and described in depth. To capture the emerging trend in mass manufacturing of 2D materials, we review the research progress on biomaterial-assisted exfoliation. Finally, we present a critical assessment of newly developed 2D biomaterials in biomedical applications.

Conductance and tunnelling current characteristics for individual identification of synthetic nucleic acids with a graphene device

Based on combined density functional theory and non-equilibrium Green's function quantum transport studies, in the present work we have demonstrated the quantum interference (QI) effect on the transverse conductance of Hachimoji (synthetic) nucleic acids when placed between the oxygen-terminated zigzag graphene nanoribbon (O-ZGNR) nanoelectrodes. We theorize that the QI effect could be well preserved in π-π coupling between a target nucleobase molecule and the carbon-based nanoelectrodes. Our study indicates that the QI effect, such as anti-resonance or Fano-resonance, affects the variation of transverse conductance depending on the nucleobase conformation. Furthermore, a variation of up to 2-5 orders of magnitude is observed in the conductance upon rotation for all the nucleobases. The current-voltage (I-V) characteristics results suggest a distinct variation in the electronic tunnelling current across the proposed nanogap device for all five nucleobases with the applied bias voltage ranges from 0.1-1.0 V. The different rotation angles keep the distinct feature of the nucleobases in both transverse conductance and tunnelling current features. Both features could be utilized in an accurate synthetic DNA sequencing device.

The application of single molecule nanopore sensing for quantitative analysis

Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.

Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control

We present an electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA. Previously developed "DNA flossing" control logic generates multiple scans of each captured DNA. We extended this logic in two ways: first, to automate "zooming out" on each molecule to progressively increase the number of tags scanned during flossing, and second, to automate recapture of a molecule that exited flossing to enable interrogation of the same and/or different regions of the molecule. Custom analysis methods were developed to produce consensus alignments from each multiscan event. The combined multiscanning and multicapture method was applied to the challenge of mapping from a heterogeneous mixture of single-molecule fragments that make up the Escherichia coli (E. coli) chromosome. Coverage of 3.1× across 2355 resolvable sites of the E. coli genome was achieved after 5.6 h of recording time. The recapture method showed a 38% increase in the merged-event alignment length compared to single-scan alignments. The observed intertag resolution was 150 bp in engineered DNA molecules and 166 bp natively within fragments of E. coli DNA, with detection of 133 intersite intervals shorter than 200 bp in the E. coli reference map. We present results on estimating distances in repetitive regions of the E. coli genome. With an appropriately designed array, higher throughput implementations could enable human-sized genome and epigenome mapping applications.

Highly Enhanced Photoluminescence of Monolayer MoS2 in Plasmonic Hybrids with Double-Layer Stacked Ag Nanoparticles

In this work, a feasible method was proposed to prepare MoS₂-based plasmonic hybrid systems with high photoluminescence (PL) emission enhancement. The enhancement effect of plasmonic hybrids on the PL emission of MoS₂ has been systematically studied on MoS₂/Ag spherical nanoparticle (SP) hybrid systems with different architectures by changing the stacking position of Ag SPs. It is demonstrated that the sandwich-like hybrid composed of monolayer MoS₂ and dielectric Al₂O₃ layer between two layers of Ag SPs has the highest PL enhancement. Remarkably, after adding an Al₂O₃ layer under MoS₂, the PL intensity enhancement up to 209 times was achieved in the sandwich-like hybrid system. Compared with the hybrid with single-layer SPs, the sandwich-like hybrid system with double-layer Ag SPs exhibited an obvious blue shift as a result of the selective enhancement of the A⁰ exciton in MoS₂. These results demonstrate that MoS₂/Ag SP hybrid nanosystems have significant implications for sensing and photoelectronic devices.

DNA sequencing based on electronic tunneling in a gold nanogap: a first-principles study

Deoxyribonucleic acid (DNA) sequencing has found wide applications in medicine including treatment of diseases, diagnosis and genetics studies. Rapid and cost-effective DNA sequencing has been achieved by measuring the transverse electronic conductance as a single-stranded DNA is driven through a nanojunction. With the aim of improving the accuracy and sensitivity of DNA sequencing, we investigate the electron transport properties of DNA nucleobases within gold nanogaps based on first-principles quantum transport simulations. Considering the fact that the DNA bases can rotate within the nanogap during measurements, different nucleobase orientations and their corresponding residence time within the nanogap are explicitly taken into account based on their energetics. This allows us to obtain an average current that can be compared directly to experimental measurements. Our results indicate that bare gold electrodes show low distinguishability among the four DNA nucleobases while the distinguishability can be substantially enhanced with sulfur atom decorated electrodes. We further optimized the size of the nanogap by maximizing the residence time of the desired orientation.

Single-layer membranes for organic solvent nanofiltration: a molecular dynamics simulation and comparative experimental study

Organic solvents are widely used in pharmaceutical and chemical industries. Their separation and recovery account for a large part of energy consumption and capital cost in many industrial processes. MoS₂ membranes with varying pore sizes (0.6 nm pore with S atoms, 0.7 nm pore with Mo atoms, 1.3 nm pore with S atoms, 1.4 nm pore with Mo atoms) were investigated as organic solvent nanofiltration (OSN) membranes using molecular simulation in this study. The fluxes of five polar solvents (methanol, ethanol, propanol, acetonitrile and acetone) and a nonpolar solvent (n-hexane) were predicted. Although the 0.6 nm S pore has a smaller pore size, it has a better flux for some organic solvents than the 0.7 nm Mo pore. This selective behavior of molybdenum disulfide was confirmed by calculating the potential of mean force (PMF) of each solvent molecule. The PMFs show that polar solvents face a higher energy barrier through the pore, and greater resistance needs to be overcome. After testing the permeability of solvent by experiment and simulation, the flux changes of different solvents have the same trend in experiment and simulation. The solvent permeability was slightly affected in the presence of solute (acetaminophen), and MoS₂ membranes with small pores demonstrated 100% rejection rate for acetaminophen. This study confirmed that pore chemistry and pore size play important roles in OSN, and MoS₂ is a promising OSN membrane for the recovery of organic solvents.

Cataloguing the proteome: Current developments in single-molecule protein sequencing

The cellular proteome is complex and dynamic, with proteins playing a critical role in cell-level biological processes that contribute to homeostasis, stimuli response, and disease pathology, among others. As such, protein analysis and characterization are of extreme importance in both research and clinical settings. In the last few decades, most proteomics analysis has relied on mass spectrometry, affinity reagents, or some combination thereof. However, these techniques are limited by their requirements for large sample amounts, low resolution, and insufficient dynamic range, making them largely insufficient for the characterization of proteins in low-abundance or single-cell proteomic analysis. Despite unique technical challenges, several single-molecule protein sequencing (SMPS) technologies have been proposed in recent years to address these issues. In this review, we outline several approaches to SMPS technologies and discuss their advantages, limitations, and potential contributions toward an accurate, sensitive, and high-throughput platform.

Predicting Biomolecule Adsorption on MoS2 Nanosheets with High Structural Fidelity

A new force field, MoSu-CHARMM, for the description of bio-interfacial structures at the aqueous MoS2 interface is developed, based on quantum chemical data. The force field describes non-covalent interactions between...

High Directional Water Transport Graphene Oxide Biphilic Stack

Understanding the nature of water transport in nanoscale is of high importance. Graphene properties such as mass flow rate, stability, filtration efficiency, and selectivity have been studied in various fields. It is a widely held view that the hydrophilicity of graphene oxide enhances the water transport properties. In this study, it is shown that despite this belief, a combination of graphene and graphene oxide can yield superior transport properties including high mass flow rate and directionality. Firstly, different membrane characteristics such as the smallest pore diameter for water molecules sieving and mass flow rate have been evaluated. Furthermore, a combination of graphene and graphene oxide, a biphilic stack of hydrophobic and hydrophilic layers, are used to evaluate the mass flow rates and results are compared with that of normal graphene oxide laminates. The proposed structure acts like a water diode i.e. conduct water molecules in a desired direction and increases the mass flow rate several times. The effect of interatomic potential, oxidation level and charge, and the spacing between layers on both mass flow rate and directionality are examined. It is found that an optimized structure conducts water in a desired direction and increases the mass flow rate up to 10 times for the small interlayer distance of 7 Å compared to the normal graphene oxide laminates. The given structures can be used in a wide range of filtration applications where selective water sieving with high mass flow rate is desired.

Comparison of water desalination performance of porous graphene and MoS2 nanosheets

Following graphene and its derivatives, molybdenum disulfide (MoS₂) has become a research hotspot in two-dimensional materials. Both graphene and MoS₂ exhibit great potential in water treatment. A variety of nanoporous graphene or MoS₂ membranes have been designed for water desalination. In this work, we compared the water flux and ion rejection of MoS₂ and graphene nanopores, using molecular dynamics simulations. The simulation results demonstrate that monolayer nanopores have higher water fluxes than bilayer nanopores with lower ion rejection rates. MoS₂ nanopores perform better than graphene in terms of water permeability. Exploration of the underlying mechanism indicates that the water molecules in the MoS₂ pores have faster velocity and higher mass density than those in the graphene pores, due to the outer hydrophobic and inner hydrophilic edges of MoS₂ pores. In addition, increasing the polarity of the pore edge causes a decrease in water flux while enhancement of ion rejection. Our findings may provide theoretical guidance for the design of MoS₂ membranes in water purification.

(1) The water flux of MoS₂ is higher than that of graphene with similar pore area regardless of whether monolayer or bilayer. (2) A monolayer has higher water flux than a bilayer. In contrast, a monolayer has lower ion rejection than a bilayer.

Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing

Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.

Exploiting the optical sensing of fluorophore-tagged DNA nucleobases on hexagonal BN and Al-doped BN sheets: a computational study

Hexagonal boron nitride (h-BN) sheets possess high fluorescence quenching ability and high affinity towards DNA/RNA, and they can be used as a sensing platform for rapid detection. We report the absorption and emission properties of DNA nucleobases such as adenine (A), cytosine (C), guanine (G), and thymine (T) tagged with benzoxazole on h-BN and aluminium-doped h-BN (Al_hBN) sheets. The binding affinity of studied nucleobases on h-BN sheets at the M062X/6-31G* level of theory showed the following adsorption trend: G ≥ T ≥ A > C, which is in good agreement with the previous results. The calculated stability trend of nucleobases on the Al_hBN sheet follows as C > G > A > T at the same level of theory. The physically adsorbed behavior of nucleobases to h-BN sheets was confirmed by the non-covalent interactions (NCIs) and the total density of states (TDOS) plots. The NCI results indicated that van der Waals interactions contribute significantly to the adsorption of nucleobases on h-BN sheets. Atoms in molecules (AIM) calculations revealed the electrostatic interactions between nucleobases and the Al_hBN sheet. The quenching phenomenon of nucleobase-tagged fluorophores on h-BN and Al_hBN sheets was investigated by TD-DFT calculations using the same level of theory. The thymine-tagged fluorophore upon adsorption to the pristine h-BN sheet was found to be blue-shifted (∼43 nm); however, the guanine-tagged fluorophore with Al_hBN showed a remarkable difference from other nucleobase-tagged fluorophores in the absorption and emission spectrum. Guanine-tagged fluorophores showed a smaller blue shift (∼7 nm) in the absorption spectrum; however, it showed a larger red shift (∼55 nm) than the other nucleobase-tagged fluorophores on Al_hBN sheets and can be useful in recognizing a sequence-specific phenomenon as a fluorescent biosensor of DNA and RNA to ascertain the presence of such nucleobases.

Probing the adsorption behavior and free energy landscape of single-stranded DNA oligonucleotides on single-layer MoS2with molecular dynamics

Interfacing single-stranded DNA (ssDNA) with 2D transition metal dichalcogenides are important for numerous technological advancements. However, the molecular mechanism of this process, including the nature of intermolecular association and conformational details of the self-assembled hybrids is still not well understood. Here, atomistic molecular dynamics simulation is employed to study the distinct adsorption behavior of ssDNA on a single-layer MoS₂in aqueous environment. The ssDNA sequences [T₁₀, G₁₀, A₁₀, C₁₀, U₁₀, (GT)₅, and (AC)₅] are chosen on the basis that short ssDNA segments can undergo a spontaneous conformational change upon adsorption and allow efficient sampling of the conformational landscape. Differences in hybridization is attributed to the inherent molecular recognition ability of the bases. While the binding appears to be primarily driven by energetically favorable van der Waalsπ-stacking interactions, equilibrium structures are modulated by the ssDNA conformational changes. The poly-purines demonstrate two concurrently competingπ-stacking interactions: nucleobase-nucleobase (intramolecular) and nucleobase-MoS₂(intermolecular). The poly-pyrimidines, on the other hand, reveal enhancedπ-stacking interactions, thereby maximizing the number of contacts. The results provide new molecular-level understanding of ssDNA adsorption on the MoS₂surface and facilitate future studies in design of functional DNA/MoS₂structure-based platforms for DNA sequencing, biosensing (optical, electrochemical, and electronic), and drug delivery.

Structure and dynamics of nanoconfined water and aqueous solutions

This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid's structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.

Spontaneous DNA translocation through a van der Waals heterostructure nanopore for single-molecule detection

Solid-state nanopore detection and sequencing of a single molecule offers a new paradigm because of its several well-recognized features such as long reads, high throughput, high precision and direct analyses. However, several key technical challenges are yet to be addressed, especially the abilities to control the speed and direct the translocation of the target molecules. In this work, using molecular dynamics (MD) simulations, we found a spontaneous translocation of single-stranded DNA (ssDNA) through a van der Waals (vdW) heterostructure nanopore formed by stacking two graphenic materials, namely those of BC₃ and C₃N. Our results showed that, without using an external stimulus, ssDNA can be spontaneously transported through such a vdW nanopore from its BC₃ side to its C₃N side, with the C₃N surface demonstrating a stronger capability than the BC₃ surface to attract DNA bases. Thus, the distinct binding strengths of BC₃ and C₃N were concluded to drive the ssDNA translocation. The results indicated the vdW forces playing a leading role during the translocation process. Our simulations also showed, at the edges of the nanopore, a clear energy barrier for nucleotides, resulting in a translocation speed slowed to a value of 0.2 μs per base, i.e., twice as slow as that indicated for the latest published methods. The present findings provide a new architecture for biomolecule detection and sequencing, which may be considered some of the most important functions of nanomaterials in biological and chemical analyses.

Label-Free Identification of Single Mononucleotides by Nanoscale Electrophoresis

Nanoscale electrophoresis allows for unique separations of single molecules, such as DNA/RNA nucleobases, and thus has the potential to be used as single molecular sensors for exonuclease sequencing. For this to be envisioned, label-free detection of the nucleotides to determine their electrophoretic mobility (i.e., time-of-flight, TOF) for highly accurate identification must be realized. Here, for the first time a novel nanosensor is shown that allows discriminating four 2-deoxyribonucleoside 5'-monophosphates, dNMPs, molecules in a label-free manner by nanoscale electrophoresis. This is made possible by positioning two sub-10 nm in-plane pores at both ends of a nanochannel column used for nanoscale electrophoresis and measuring the longitudinal transient current during translocation of the molecules. The dual nanopore TOF sensor with 0.5, 1, and 5 µm long nanochannel column lengths discriminates different dNMPs with a mean accuracy of 55, 66, and 94%, respectively. This nanosensor format can broadly be applicable to label-free detection and discrimination of other single molecules, vesicles, and particles by changing the dimensions of the nanochannel column and in-plane nanopores and integrating different pre- and postprocessing units to the nanosensor. This is simple to accomplish because the nanosensor is contained within a fluidic network made in plastic via replication.

Velocity control of protein translocation through a nanopore by tuning the fraction of benzenoid residues

Protein sequencing is essential to unveil the mechanism of cellular processes that govern the function of living organisms, and which play a crucial role in the field of drug design and molecular diagnostics. Nanopores have been proved to be effective tools in single molecule sensing, but the fast translocation speed of a peptide through a nanopore is one of the major obstacles that hinders the development of nanopore-based protein sequencing. In this work, by using molecular dynamics simulations (MDS) it is found that the peptide containing more hydrophobic residues permeates slower through a molybdenum disulfide nanopore, which originates from the strong interaction between the membrane surface and the hydrophobic residues. The binding affinity is remarkable especially for benzenoid residues as they contain a hydrophobic aromatic ring that is composed of relatively non-polar C-C and C-H bonds. By tuning the fraction of benzenoid residues of the peptide, the velocity of the protein translocation through the nanopore is well controlled. The peptide with all the hydrophobic residues being benzenoid residues is found to translocate through the nanopore almost ten times slower than the one without any benzenoid residues, which is beneficial for gathering adequate information for precise amino acid identification.

Nanopore Data Analysis: Baseline Construction and Abrupt Change-Based Multilevel Fitting

Solid-state nanopore technology delivers single-molecule resolution information, and the quality of the deliverables hinges on the capability of the analysis platform to extract maximum possible events and fit them appropriately. In this work, we present an analysis platform with four baseline fitting methods adaptive to a wide range of nanopore traces (including those with a step or abrupt changes where pre-existing platforms fail) to maximize extractable events (2× improvement in some cases) and multilevel event fitting capability. The baseline fitting methods, in the increasing order of robustness and computational cost, include arithmetic mean, linear fit, Gaussian smoothing, and Gaussian smoothing and regressed mixing. The performance was tested with ultra-stable to vigorously fluctuating current profiles, and the event count increased with increasing fitting robustness prominently for vigorously fluctuating profiles. Turning points of events were clustered using the dbscan method, followed by segmentation into preliminary levels based on abrupt changes in the signal level, which were then iteratively refined to deduce the final levels of the event. Finally, we show the utility of clustering for multilevel DNA data analysis, followed by the assessment of protein translocation profiles.

Sub-10-nm-thick SiN nanopore membranes fabricated using the SiO2sacrificial layer process

In our previous studies, ultrathin SiN membranes down to 3 nm in thickness were fabricated using the poly-Si sacrificial layer process, and nanopores were formed in those membranes. The region of the SiN membrane fabricated using this process was small, and the poly-Si sacrificial layer remained throughout the other region. On the other hand, to reduce the noise of the current through the nanopore, it is preferable to reduce the capacitance of the nanopore chip by replacing the poly-Si layer with an insulator with low permittivity, such as SiO₂. Thus, in this study, the fabrication of SiN membranes with thicknesses of 3-7 nm using the SiO₂sacrificial layer process was examined. SiN membranes with thicknesses of less than 5 nm could not be formed when the thickness of the top SiN layer deposited onto the sacrificial layer was 100 nm. In contrast, SiN membranes down to 3.07 nm in thickness could be formed when the top SiN layer was 40 nm in thickness. This is thought to be due to the difference in membrane stress. Nanopores were then fabricated in the membranes via dielectric breakdown. The current noise of the nanopore membranes was approximately 3/5 that of membranes fabricated using the poly-Si sacrificial layer process. Last, ionic current blockades were measured when poly(dT)₆₀passed through the nanopores, and the effective thickness of the nanopores was estimated based on those current-blockade values. The effective thickness was approximately 4.8 nm when the deposited thickness of the SiN membrane was 6.03 nm. On the other hand, the effective thickness and the deposited thickness were almost the same when the deposited thickness was 3.07 nm. This suggests it became difficult to form a shape in which the thickness of the nanopore edge was thinner than the deposited membrane thickness as the deposited thickness decreased.

Computer vision AC-STEM automated image analysis for 2D nanopore applications

Transmission electron microscopy (TEM) has led to important discoveries in atomic imaging and as an atom-by-atom fabrication tool. Using electron beams, atomic structures can be patterned, annealed and crystallized, and nanopores can be drilled in thin membranes. We review current progress in TEM analysis and implement a computer vision nanopore-detection algorithm that achieves a 96% pixelwise precision in TEM images of nanopores in 2D membranes (WS₂), and discuss parameter optimization including a variation on the traditional grid search and gradient ascent. Such nanopores have applications in ion detection, water filtration, and DNA sequencing, where ionic conductance through the pore should be concordant with its TEM-measured size. Standard computer vision methods have their advantages as they are intuitive and do not require extensive training data. For completeness, we briefly comment on related machine learning for 2D materials analysis and discuss relevant progress in these fields. Image analysis alongside TEM allows correlated fabrication and analysis done simultaneously in situ to engineer devices at the atomic scale.

Tuning Protein Discrimination Through Altering the Sampling Interface Formed between the Analyte and the OmpG Nanopore

Nanopore sensors capable of distinguishing homologous protein analytes are highly desirable tools for proteomics research and disease diagnostics. Recently, an engineered outer membrane protein G (OmpG) nanopore with a high-affinity ligand attached to a gating loop 6 showed specificity for distinguishing homologous proteins in complex mixtures. Here, we report the development of OmpG nanopores with the other six loops used as the anchoring point to host an affinity ligand for protein sensing. We investigated how the analyte binding to the affinity ligand located at different loops affects the detection sensitivity, selectivity, and specificity. Our results reveal that analytes weakly attracted to the OmpG nanopore surface are only detectable when the ligand is tethered to loop 6. In contrast, protein analytes that form a strong interaction with the OmpG surface via electrostatic attractions are distinguishable by all seven OmpG nanopore constructs. In addition, the same analyte can generate distinct binding signals with different OmpG nanopore constructs. The ability to exploit all seven OmpG loops will aid the design of a new generation of OmpG sensors with increased sensitivity, selectivity, and specificity for biomarker sensing.

DNA Detection with Single-Layer Ti3C2 MXene Nanopore

Nanopore based sequencing is an exciting alternative to the conventional sequencing methods as it allows for high-throughput sequencing with lower reagent costs and time requirements. Biological nanopores, such as α-hemolysin, are subject to breakdown under thermal, electrical, and mechanical stress after being used millions of times. On the contrary, two-dimensional (2D) nanomaterials have been explored as a solid-state platform for the sequencing of DNA. Their subnanometer thickness and outstanding mechanical properties have made possible the high-resolution and high-signal-to-noise ratio detection of DNA, but such a performance is dependent on the type of nanomaterial selected. Solid-state nanopores of graphene, Si₃N₄, and MoS₂ have been studied as potential candidates for DNA detection. However, it is important to understand the sensitivity and characterization of these solid-state materials for nanopore based detection. Recent developments in the synthesis of MXene have inspired our interest in its application as a nanopore based DNA detection membrane. Here, we simulate the metal carbide, MXene (Ti₃C₂), with single stranded DNA to understand its interactions and the efficiency of MXene as a putative material for the development of a nanopore based detection platform. Using molecular dynamics (MD) simulations, we present evidence that a MXene based nanopore is able to detect the different types of DNA bases. We have successfully identified features to differentiate the translocation of different types of DNA bases across the nanopore.

Force fields for water-surface interaction: is reproduction of the experimental water contact angle enough?

A new protocol based on quantum chemical calculations and molecular dynamics simulations is proposed to revisit water-MoS₂ interfacial force fields (FFs). The accurate reproduction of experimental water contact angles is suggested to be insufficient to ensure reliable FFs for recovering structural properties of the interfacial solvent. As an example, this protocol is used to develop a new set of FF parameters to both capture interfacial structural phenomena at the interface between water and MoS₂ and recover experimental water contact angle data. This approach can be applied to any interface where contact angle data are available.

Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases

Over the last decade, we have been witnessing the rise of two-dimensional (2D) materials. Several 2D materials with outstanding properties have been theoretically predicted and experimentally synthesized. 2D materials are good candidates for sensing and detecting various biomolecules because of their extraordinary properties, such as a high surface-to-volume ratio. Silicene and germanene are the monolayer honeycomb structures of silicon and germanium, respectively. Quantum simulations have been very effective in understanding the interaction mechanism of 2D materials and biomolecules and may play an important role in the development of effective and reliable biosensors. This article focuses on understanding the interaction of DNA/RNA nucleobases with silicene and germanane monolayers and obtaining the possibility of using silicene and germanane monolayers as a biosensor for DNA/RNA nucleobases' sequencing using the first principle of Density Functional Theory (DFT) calculations with van der Waals (vdW) correction and nonequilibrium Green's function method. Guanine (G), Cytosine (C), Adenine (A), Thymine (T), and Uracil (U) were examined as the analytes. The strength of adsorption between the DNA/RNA nucleobases and silicene and germanane is G > C > A > T > U. Moreover, our recent work on the investigation of Au- and Li-decorated silicene and germanane for detection of DNA/RNA nucleobases is presented. Our results show that it is possible to get remarkable changes in transmittance due to the adsorption of nucleobases, especially for G, A, and C. These results indicate that silicene and germanene are both good candidates for the applications in fast sequencing devices for DNA/RNA nucleobases. Additionally, our present results have the potential to give insight into experimental studies and can be valuable for advancements in biosensing and nanobiotechnology.

Identifying DNA Nucleotides via Transverse Electronic Transport in Atomically Thin Topologically Defected Graphene Electrodes

Extended line defects in graphene (ELDG) sheets have been found to be promising for biomolecule sensing applications. By means of the consistent-exchange van der Waals density-functional (vdW-DF-cx) method, the electronic, structural, and quantum transport properties of the ELDG nanogap setup has been studied when a DNA nucleotide molecule is positioned inside the nanogap electrodes. The interaction energy (E_i) values indicate charge transfer interaction between the nucleotide molecule and electrode edges. The charge density difference plots reveal that charge fluctuates around the ELDG nanogap edges adjacent to the nucleotides. This charge redistribution grounds the modulation of electronic charge transport in the ELDG nanogap device. Further, we study the electronic transverse-conductance and tunnelling current-voltage (I-V) characteristics across two closely spaced ELDG nanogap electrodes using the density functional theory and the nonequilibrium Green's function methods when a DNA nucleotide is translocated through the nanogap. Our outcomes indicate that the ELDG nano gap device could allow sequencing of DNA nucleotides with a robust and consistent yield, giving the tunneling electric current signals that vary by more than 1 order of magnitude electric current (I) for the different DNA nucleotides. So, we predict that the ELDG nanogap-based tunneling device can be suitable for sequencing DNA nucleobases.

Single Nucleotides Moving through Nanoslits Composed of Self-Assembled Monolayers via Equilibrium and Nonequilibrium Molecular Dynamics

Nonequilibrium molecular dynamics (MD) simulations were used to study the effect of three chemical surface groups on the separation of DNA mononucleotide velocity (or time-of-flight) distributions as they pass through nanoslits. We used nanoslits functionalize with self-assembled monolayers (SAMs) since they have relatively smooth surfaces. The SAM molecules were terminated with either a methyl, methylformyl, or phenoxy group, and the nucleotides were driven electrophoretically with an electric field intensity of 0.1 V/nm in slits about 3 nm wide. Although these large driving forces are physically difficult to achieve experimentally, the simulations are still of great value as they provide molecular level insight into nucleotide translocation events and allow comparison of different surfaces. Nucleotides adsorbed and desorbed from the slit surface multiple times during the simulations. The required slit length for 99% accuracy in identifying the deoxynucleotide monophosphates (dNMPs), based on the separation of the distributions of time of flight, was used to compare the surfaces with shorter lengths indicating more efficient separation. The lengths were 6.5 μm for phenoxy-terminated SAMs, 270 μm for methylformyl-terminated SAMs, and 2400 μm for methyl-terminated SAMs. Our study showed that a slit with a section with methyl termination and the second section with methylformyl termination lead to a required length of 120 μm, which was significantly lower than for only a methylformyl- or methyl-terminated surface.

Electroosmotic flow: From microfluidics to nanofluidics

Electroosmotic flow (EOF), a consequence of an imposed electric field onto an electrolyte solution in the tangential direction of a charged surface, has emerged as an important phenomenon in electrokinetic transport at the micro/nanoscale. Because of their ability to efficiently pump liquids in miniaturized systems without incorporating any mechanical parts, electroosmotic methods for fluid pumping have been adopted in versatile applications—from biotechnology to environmental science. To understand the electrokinetic pumping mechanism, it is crucial to identify the role of an ionically polarized layer, the so‐called electrical double layer (EDL), which forms in the vicinity of a charged solid–liquid interface, as well as the characteristic length scale of the conducting media. Therefore, in this tutorial review, we summarize the development of electrical double layer models from a historical point of view to elucidate the interplay and configuration of water molecules and ions in the vicinity of a solid–liquid interface. Moreover, we discuss the physicochemical phenomena owing to the interaction of electrical double layer when the characteristic length of the conducting media is decreased from the microscale to the nanoscale. Finally, we highlight the pioneering studies and the most recent works on electro osmotic flow devoted to both theoretical and experimental aspects.