Versatile ultrathin nanoporous silicon nitride membranes

Nanopores for DNA and biomolecule analysis: Diagnostic, genomic insights, applications in energy conversion and catalysis

Recently, nanopores have emerged as highly significant structures with broad applications in diverse scientific and technological fields. They can naturally occur in biological membranes or be artificially fabricated using advanced techniques. Recent advances in nanopore technology have revolutionized genomics by offering previously unheard-of capacities for deoxyribo nucleic acid (DNA) sequencing and analysis. These tiny pores allow individual molecules to be found more easily, allowing for real-time DNA analysis and providing currently unheard-of insights into genetics and diagnostics. By tracking alterations in electrical or ionic currents as biomolecules traverse the pore, nanopores make possible the real-time recognition of other biomolecules, like proteins, nucleic acids, and small molecules, eliminating the need for labeling. This label-free detection potential holds a huge promise in medical diagnostics, genotyping, environmental monitoring, etc. Nanopores have significantly improved DNA sequencing technology such as increment in read length, enabling researchers to sequence entire genomic regions, accuracy can be improved and recent updates have led to a reported increase in total DNA reads, demonstrating the technology's capacity for high-throughput applications via trapping individual DNA strands and monitoring the variations of ionic current as each nucleotide passes across the pore. Finally, nanopore sequencing is well-known as a novel and highly flexible technique for DNA analyses, which has a huge deal of promise in clinical diagnosis and genomics research. Hence, this review article comprehensively explains nanopores for DNA analysis and other biomolecules, their synthesis, and diverse applications.

Advances and Challenges in Solid-State Nanopores for DNA Sequencing

Solid-state nanopore sensing, a state-of-the-art technology for single-molecule detection, has rapidly advanced in recent years and demonstrates significant potential in DNA sequencing. This technology determines the nucleotide sequences by analyzing the electrical or optical signal variations that occur when DNA molecules pass through the nanopore. It offers notable advantages, including high-throughput, single-molecule detection, real-time monitoring, and the elimination of the need for polymerase chain reaction (PCR) amplification, thereby presenting broad application prospects in areas such as the diagnosis and treatment of genetic diseases. This paper reviews the solid-state nanopore DNA sequencing technology by discussing advancements in nanopore types, preparation techniques, and sequencing detection methods. It examines various nanopore materials, including silicon-based materials and two-dimensional (2D) materials, as well as preparation techniques such as transmission electron microscopy (TEM), focused ion beam (FIB) etching, and controlled breakdown (CBD). Additionally, it elucidates sequencing detection mechanisms, including ion-current blockade, transverse-current detection, and optical detection. However, this technology faces numerous challenges in its implementation and future commercialization. For instance, limited spatial resolution hampers single-base identification; the rapid translocation speed of DNA impacts time resolution; and various types of noise significantly disrupt detection signals. In response, researchers have proposed several solutions, including local thinning of the film, adjustment of surface charges, and optimization of detection materials and structures. With interdisciplinary integration and technological innovation, solid-state nanopore DNA sequencing technology is expected to make breakthroughs, bringing transformations to life sciences research and medical diagnosis.

Localized Nanopore Fabrication in Silicon Nitride Membranes by Femtosecond Laser Exposure and Subsequent Controlled Breakdown

Controlled breakdown has emerged as an effective method for fabricating solid-state nanopores in thin suspended dielectric membranes for various biomolecular sensing applications. On an unpatterned membrane, the site of nanopore formation by controlled breakdown is random. Nanopore formation on a specific site on the membrane has previously been realized using local thinning of the membrane by lithographic processes or laser-assisted photothermal etching under immersion in an aqueous salt solution. However, these approaches require elaborate and expensive cleanroom-based lithography processes or involve intricate procedures using custom-made equipment. Here, we present a rapid cleanroom-free approach using single pulse femtosecond laser exposures of 50 nm thick silicon nitride membranes in air to localize the site of nanopore formation by subsequent controlled breakdown to an area less than 500 nm in diameter on the membrane. The precise positioning of the nanopores on the membrane could be produced both using laser exposure powers which caused significant thinning of the silicon nitride membrane (up to 60% of the original thickness locally), as well as at laser powers which caused no visible modification of the membrane at all. We show that nanopores made using our approach can work as single-molecule sensors by performing dsDNA translocation experiments. Due to the applicability of femtosecond laser processing to a wide range of membrane materials, we expect our approach to simplify the fabrication of localized nanopores by controlled breakdown in a variety of thin film material stacks, thereby enabling more sophisticated nanopore sensors.

Gate-All-Around Nanopore Osmotic Power Generators

Nanofluidic channels in a membrane represent a promising avenue for harnessing blue energy from salinity gradients, relying on permselectivity as a pivotal characteristic crucial for inducing electricity through diffusive ion transport. Surface charge emerges as a central player in the osmotic energy conversion process, emphasizing the critical significance of a judicious selection of membrane materials to achieve optimal ion permeability and selectivity within specific channel dimensions. Alternatively, here we report a field-effect approach for in situ manipulation of the ion selectivity in a nanopore. Application of voltage to a surround-gate electrode allows precise adjustment of the surface charge density at the pore wall. Leveraging the gating control, we demonstrate permselectivity turnover to enhanced cation selective transport in multipore membranes, resulting in a 6-fold increase in the energy conversion efficiency with a power density of 15 W/m2 under a salinity gradient. These findings not only advance our fundamental understanding of ion transport in nanochannels but also provide a scalable and efficient strategy for nanoporous membrane osmotic power generation.

Ultralow Energy Consumption Angstrom-Fluidic Memristor

The emergence of nanofluidic memristors has made a giant leap to mimic the neuromorphic functions of biological neurons. Here, we report neuromorphic signaling using Angstrom-scale funnel-shaped channels with poly-l-lysine (PLL) assembled at nano-openings. We found frequency-dependent current-voltage characteristics under sweeping voltage, which represents a diode in low frequencies, but it showed pinched current hysteresis as frequency increases. The current hysteresis is strongly dependent on pH values but weakly dependent on salt concentration. We attributed the current hysteresis to the entropy barrier of PLL molecules entering and exiting the Angstrom channels, resulting in reversible voltage-gated open-close state transitions. We successfully emulated the synaptic adaptation of Hebbian learning using voltage spikes and obtained a minimum energy consumption of 2-23 fJ in each spike per channel. Our findings pave a new way to mimic neuronal functions by Angstrom channels in low energy consumption.

Fluids and Electrolytes under Confinement in Single-Digit Nanopores

Confined fluids and electrolyte solutions in nanopores exhibit rich and surprising physics and chemistry that impact the mass transport and energy efficiency in many important natural systems and industrial applications. Existing theories often fail to predict the exotic effects observed in the narrowest of such pores, called single-digit nanopores (SDNs), which have diameters or conduit widths of less than 10 nm, and have only recently become accessible for experimental measurements. What SDNs reveal has been surprising, including a rapidly increasing number of examples such as extraordinarily fast water transport, distorted fluid-phase boundaries, strong ion-correlation and quantum effects, and dielectric anomalies that are not observed in larger pores. Exploiting these effects presents myriad opportunities in both basic and applied research that stand to impact a host of new technologies at the water-energy nexus, from new membranes for precise separations and water purification to new gas permeable materials for water electrolyzers and energy-storage devices. SDNs also present unique opportunities to achieve ultrasensitive and selective chemical sensing at the single-ion and single-molecule limit. In this review article, we summarize the progress on nanofluidics of SDNs, with a focus on the confinement effects that arise in these extremely narrow nanopores. The recent development of precision model systems, transformative experimental tools, and multiscale theories that have played enabling roles in advancing this frontier are reviewed. We also identify new knowledge gaps in our understanding of nanofluidic transport and provide an outlook for the future challenges and opportunities at this rapidly advancing frontier.

Nanopores: synergy from DNA sequencing to industrial filtration - small holes with big impact

Nanopores in thin membranes play important roles in science and industry. Single nanopores have provided a step-change in portable DNA sequencing and understanding nanoscale transport while multipore membranes facilitate food processing and purification of water and medicine. Despite the unifying use of nanopores, the fields of single nanopores and multipore membranes differ - to varying degrees - in terms of materials, fabrication, analysis, and applications. Such a partial disconnect hinders scientific progress as important challenges are best resolved together. This Viewpoint suggests how synergistic crosstalk between the two fields can provide considerable mutual benefits in fundamental understanding and the development of advanced membranes. We first describe the main differences including the atomistic definition of single pores compared to the less defined conduits in multipore membranes. We then outline steps to improve communication between the two fields such as harmonizing measurements and modelling of transport and selectivity. The resulting insight is expected to improve the rational design of porous membranes. The Viewpoint concludes with an outlook of other developments that can be best achieved by collaboration across the two fields to advance the understanding of transport in nanopores and create next-generation porous membranes tailored for sensing, filtration, and other applications.

Double-sided plasmonic metasurface for simultaneous biomolecular separation and SERS detection

Porous membrane-based nanofiltration separation of small biomolecules is a widely used biotechnology for which size-based selectivity is a critical parameter of technological relevance. Efficient determination of size selectivity calls for an advanced detection method capable of performing sensitive, rapid, and on-membrane examination. Surface-enhanced Raman spectroscopy (SERS) is such a detection method that has been widely recognized as an ultrasensitive technique for trace-level detection with sensitivity down to the single-molecule level. In this work, we for the first time develop a double-sided hierarchical porous membrane-like plasmonic metasurface to realize high-selectivity bimolecular separation and simultaneous ultrasensitive SERS detection. This highly flexible device, consisting of subwavelength nanocone pairs surrounded by randomly orientated sub-5 nm nanogrooves, was prepared by combining customized "top-down" fabrication of conical nanopores in an ion-track registered polycarbonate membrane and self-assembly of nanogrooves on the membrane surface through physical vapor deposition. The unique tip-to-tip oriented conical nanopores in the device enables excellent size-based molecular selectivity; the hierarchical groove-pore structure supports a peculiar cascaded electromagnetic near-field enhancement mechanism, endowing the device with SERS-based molecular detection of ultrahigh sensitivity, uniformity, repeatability, and polarization independence. With such dual structural merits and performance enhancement, we demonstrate effective nanofiltration separation of small-sized adenine from big-sized ss-DNA and synergistic SERS determination of their species. We experimentally demonstrate an ultrasensitive detection of 4-mercaptopyridine down to 10 pM. Together with its unparalleled mechanical flexibility, this double-side-responsive plasmonic metasurface membrane can find great potential in real-world molecular filtration and detection under extremely complex working conditions.

Fabrication of solid-state nanopores

Nanopores are valuable single-molecule sensing tools that have been widely applied to the detection of DNA, RNA, proteins, viruses, glycans, etc. The prominent sensing platform is helping to improve our health-related quality of life and accelerate the rapid realization of precision medicine. Solid-state nanopores have made rapid progress in the past decades due to their flexible size, structure and compatibility with semiconductor fabrication processes. With the development of semiconductor fabrication techniques, materials science and surface chemistry, nanopore preparation and modification technologies have made great breakthroughs. To date, various solid-state nanopore materials, processing technologies, and modification methods are available to us. In the review, we outline the recent advances in nanopores fabrication and analyze the virtues and limitations of various membrane materials and nanopores drilling techniques.

Biomimetic Nanochannels: From Fabrication Principles to Theoretical Insights

Biological nanochannels which can regulate ionic transport across cell membranes intelligently play a significant role in physiological functions. Inspired by these nanochannels, numerous artificial nanochannels have been developed during recent years. The exploration of smart solid-state nanochannels can lay a solid foundation, not only for fundamental studies of biological systems but also practical applications in various fields. The basic fabrication principles, functional materials, and diverse applications based on artificial nanochannels are summarized in this review. In addition, theoretical insights into transport mechanisms and structure-function relationships are discussed. Meanwhile, it is believed that improvements will be made via computer-guided strategy in designing more efficient devices with upgrading accuracy. Finally, some remaining challenges and perspectives for developments in both novel conceptions and technology of this inspiring research field are stated.

Optical Nanopore Sensors for Quantitative Analysis

Nanopore sensors have received significant interest for the detection of clinically important biomarkers with single-molecule resolution. These sensors typically operate by detecting changes in the ionic current through a nanopore due to the translocation of an analyte. Recently, there has been interest in developing optical readout strategies for nanopore sensors for quantitative analysis. This is because they can utilize wide-field microscopy to independently monitor many nanopores within a high-density array. This significantly increases the amount of statistics that can be obtained, thus enabling the analysis of analytes present at ultralow concentrations. Here, we review the use of optical nanopore sensing strategies for quantitative analysis. We discuss optical nanopore sensing assays that have been developed to detect clinically relevant biomarkers, the potential for multiplexing such measurements, and techniques to fabricate high density arrays of nanopores with a view toward the use of these devices for clinical applications.

Bio-inspired Track-Etched Polymeric Nanochannels: Steady-State Biosensors for Detection of Analytes

Bio-inspired polymeric nanochannel (also referred as nanopore)-based biosensors have attracted considerable attention on account of their controllable channel size and shape, multi-functional surface chemistry, unique ionic transport properties, and good robustness for applications. There are already very informative reviews on the latest developments in solid-state artificial nanochannel-based biosensors, however, which concentrated on the resistive-pulse sensing-based sensors for practical applications. The steady-state sensing-based nanochannel biosensors, in principle, have significant advantages over their counterparts in term of high sensitivity, fast response, target analytes with no size limit, and extensive suitable range. Furthermore, among the diverse materials, nanochannels based on polymeric materials perform outstandingly, due to flexible fabrication and wide application. This compressive Review summarizes the recent advances in bio-inspired polymeric nanochannels as sensing platforms for detection of important analytes in living organisms, to meet the high demand for high-performance biosensors for analysis of target analytes, and the potential for development of smart sensing devices. In the future, research efforts can be focused on transport mechanisms in the field of steady-state or resistive-pulse nanochannel-based sensors and on developing precisely size-controlled, robust, miniature and reusable, multi-functional, and high-throughput biosensors for practical applications. Future efforts should aim at a deeper understanding of the principles at the molecular level and incorporating these diverse pore architectures into homogeneous and defect-free multi-channel membrane systems. With the rapid advancement of nanoscience and biotechnology, we believe that many more achievements in nanochannel-based biosensors could be achieved in the near future, serving people in a better way.

Nanopore-Based Power Generation from Salinity Gradient: Why It Is Not Viable

In recent years, the development of nanopore-based membranes has revitalized the prospect of harvesting salinity gradient (blue) energy. In this study, we systematically analyze the energetic performance of nanopore-based power generation (NPG) at various process scales, beginning with a single nanopore, followed by a multipore membrane coupon, and ending with a full-scale system. We confirm the high power densities attainable by a single nanopore and demonstrate that, at the coupon scale and above, concentration polarization severely hinders the power density of NPG, revealing the common, yet significant, error in linearly extrapolating single-pore performance to multipore membranes. Through our consideration of concentration polarization, we also importantly show that the development of materials with exceptional nanopore properties provides limited enhancement of practical process performance. For a full-scale NPG membrane module, we find an inherent tradeoff between power density and thermodynamic energy efficiency, whereby achieving a high power density sacrifices the energy efficiency. Furthermore, we derive a simple expression for the theoretical maximum energy efficiency of NPG, showing it is solely related to the membrane selectivity (i.e., S²/2). Through this relation, it is apparent that the energy efficiency of NPG is limited to only 50% (for a completely selective membrane, i.e., S = 1), reinforcing our optimistic full-scale simulations which result in a (practical) maximum energy efficiency of 42%. Finally, we assess the net extractable energy of a full-scale NPG system which mixes river water and seawater by including the energy losses from pretreatment and pumping, revealing that the NPG process-both in its current state of development and in the case of highly optimistic performance with minimized external energy losses-is not viable for power generation.

Ion track etching of polycarbonate membranes monitored by in situ small angle X-ray scattering

In situ small angle X-ray scattering (SAXS) measurements of ion track etching in polycarbonate foils are used to directly monitor the selective dissolution of ion tracks with high precision, including the early stages of etching. Detailed information about the track etching kinetics and size, shape, and size distribution of an ensemble of nanopores is obtained. Time resolved measurements as a function of temperature and etchant concentration show that the pore radius increases almost linearly with time for all conditions and the etching process can be described by an Arrhenius law. The radial etching shows a power law dependency on the etchant concentration. An increase in the etch rate with increasing temperature or concentration of the etchant reduces the penetration of the etchant into the polymer but does not affect the pore size distribution. The in situ measurements provide an estimate for the track etch rate, which is found to be approximately three orders of magnitude higher than the radial etch rate. The measurement methodology enables new experiments studying membrane fabrication and performance in liquid environments.

Nanostructured-membrane electron phase plates

Electron beams can acquire designed phase modulations by passing through nanostructured material phase plates. These phase modulations enable electron wavefront shaping and benefit electron microscopy, spectroscopy, lithography, and interferometry. However, in the fabrication of electron phase plates, the typically used focused-ion-beam-milling method limits the fabrication throughput and hence the active area of the phase plates. Here, we fabricated large-area electron phase plates with electron-beam lithography and reactive-ion-etching. The phase plates are characterized by electron diffraction in transmission electron microscopes with various electron energies, as well as diffractive imaging in a scanning electron microscope. We found the phase plates could produce a null in the center of the bright-field based on coherent interference of diffractive beams. Our work adds capabilities to the fabrication of electron phase plates. The nullification of the direct beam and the tunable diffraction efficiency demonstrated here also paves the way towards novel dark-field electron-microscopy techniques.

Chemically tailoring nanopores for single-molecule sensing and glycomics

A nanopore can be fairly-but uncharitably-described as simply a nanofluidic channel through a thin membrane. Even this simple structural description holds utility and underpins a range of applications. Yet significant excitement for nanopore science is more readily ignited by the role of nanopores as enabling tools for biomedical science. Nanopore techniques offer single-molecule sensing without the need for chemical labelling, since in most nanopore implementations, matter is its own label through its size, charge, and chemical functionality. Nanopores have achieved considerable prominence for single-molecule DNA sequencing. The predominance of this application, though, can overshadow their established use for nanoparticle characterization and burgeoning use for protein analysis, among other application areas. Analyte scope continues to be expanded, and with increasing analyte complexity, success will increasingly hinge on control over nanopore surface chemistry to tune the nanopore, itself, and to moderate analyte transport. Carbohydrates are emerging as the latest high-profile target of nanopore science. Their tremendous chemical and structural complexity means that they challenge conventional chemical analysis methods and thus present a compelling target for unique nanopore characterization capabilities. Furthermore, they offer molecular diversity for probing nanopore operation and sensing mechanisms. This article thus focuses on two roles of chemistry in nanopore science: its use to provide exquisite control over nanopore performance, and how analyte properties can place stringent demands on nanopore chemistry. Expanding the horizons of nanopore science requires increasing consideration of the role of chemistry and increasing sophistication in the realm of chemical control over this nanoscale milieu.

Electric-Field-Induced Ionic Sieving at Planar Graphene Oxide Heterojunctions for Miniaturized Water Desalination

Layered graphene oxide membranes (GOMs) offer a unique platform for precise sieving of small ions and molecules due to controlled sub-nanometer-wide interlayer distance and versatile surface chemistry. Pristine and chemically modified GOMs effectively block organic dyes and nanoparticles, but fail to exclude smaller ions with hydrated diameters less than 9 Å. Toward sieving of small inorganic salt ions, a number of strategies are proposed by reducing the interlayer spacing down to merely several angstroms. However, one critical challenge for such compressed GOMs is the extremely low water flux (<0.1 Lm^-2 h^-1 bar^-1 ) that prevents these innovative nanomaterials from being used in real-world applications. Here, a planar heterogeneous graphene oxide membrane (PHGOM) with both nearly perfect salt rejection and high water flux is reported. Horizontal ion transport through oppositely charged GO multilayer lateral heterojunction exhibits bi-unipolar transport behavior, blocking the conduction of both cations and anions. Assisted by a forward electric field, salt concentration is depleted in the near-neutral transition area of the PHGOM. In this situation, deionized water can be extracted from the depletion zone. Following this mechanism, a high rejection rate of 97.0% for NaCl and water flux of 1529 Lm^-2 h^-1 bar^-1 at the outlet via an inverted T-shaped water extraction mode are achieved.

Fabrication of a Biomimetic Nanochannel Logic Platform and Its Applications in the Intelligent Detection of miRNA Related to Liver Cancer

Nanochannel-based analytical techniques have great potential applications for nucleic acid sequencing and high sensitivity detection of biological molecules. However, the sensitivity of conventional solid-state nanochannel sensors is hampered by a lack of effective signal amplification strategies, which has limited its utility in the field of analytical chemistry. Here we selected a solid-state nanochannnel modified with polyethylenimine and Zr⁴⁺ in combination with graphene oxide as the sensing platform. The high-performance sensor is based upon the change of the surface charge of the nanochannel, which is resulted from DNA cascade signal amplification in solution. The target miRNA (miR-122) can be indirectly quantitated with a detection limit of 97.2 aM with an excellent selectivity. Depending on the nucleic acid's hybridization and configuration transform, the designed nanochannel sensing systems can realize the intelligent detection of multiple liver cancer-related miRNA (miR-122 and miR Let-7a) integrating with cascaded INHIBIT-OR logic gate to provide theoretical guidance and technical support for clinical diagnosis and therapeutic evaluation of liver cancer.

Ionic amplifying circuits inspired by electronics and biology

Integrated circuits are present in all electronic devices, and enable signal amplification, modulation, and relay. Nature uses another type of circuits composed of channels in a cell membrane, which regulate and amplify transport of ions, not electrons and holes as is done in electronic systems. Here we show an abiotic ionic circuit that is inspired by concepts from electronics and biology. The circuit amplifies small ionic signals into ionic outputs, and its operation mimics the electronic Darlington amplifier composed of transistors. The individual transistors are pores equipped with three terminals including a gate that is able to enrich or deplete ions in the pore. The circuits we report function at gate voltages < 1 V, respond to sub-nA gate currents, and offer ion current amplification with a gain up to ~300. Ionic amplifiers are a logical step toward improving chemical and biochemical sensing, separations and amplification, among others.

Redox-Driven Reversible Gating of Solid-State Nanochannels

The design of an electrochemically addressable nanofluidic diode is proposed, which allows tunable and nanofluidic operations via redox gating under electrochemical control. The fabrication process involves the modification of an asymmetric gold-coated solid-state nanopore with a thin layer of a redox polymer, poly(vinylferrocene) (PVFc). The composite nanochannel acts as a gate electrode by changing the electrochemical state and, consequently, the conversion/switching of ferrocene into ferricenium units upon the application of different voltages. It is shown that the electrochemical input accurately controls the surface charge density of the nanochannel walls with a predictable concomitant effect on the rectification properties. PVFc-based nanofluidic devices are able to discriminate the passage of anionic species through the nanochannel in a qualitative and quantitative manner by simply switching the redox potential of the PVFc layer. Experimental data confirmed that a rapid and reversible modulation of the ionic transport regimes can be easily attained by changing the applied potential. This applied potential plays the role of the gate voltage (V_g) in field-effect transistors (FET), so these nanofluidic channels behave as ionic FETs. Depending on the V_g values, the iontronic behavior can be switched between ohmic and diode-like regimes. We believe that this system illustrates the potential of redox-active polymers integrated into nanofluidic devices as plausible, simple, and versatile platforms to create electrochemically addressable nanofluidic devices for multiple applications.

Etched ion tracks in amorphous SiO2 characterized by small angle x-ray scattering: influence of ion energy and etching conditions

Small angle x-ray scattering was used to study the morphology of conical structures formed in thin films of amorphous SiO₂. Samples were irradiated with 1.1 GeV Au ions at the GSI UNILAC in Darmstadt, Germany, and with 185, 89 and 54 MeV Au ions at the Heavy Ion Accelerator Facility at ANU in Canberra, Australia. The irradiated material was subsequently etched in HF using two different etchant concentrations over a series of etch times to reveal conically shaped etched channels of various sizes. Synchrotron based SAXS measurements were used to characterize both the radial and axial ion track etch rates with unprecedented precision. The results show that the ion energy has a significant effect on the morphology of the etched channels, and that at short etch times resulting in very small cones, the increased etching rate of the damaged region in the radial direction with respect to the ion trajectory is significant.

Plasmonic-Nanopore Biosensors for Superior Single-Molecule Detection

Plasmonic and nanopore sensors have separately received much attention for achieving single-molecule precision. A plasmonic "hotspot" confines and enhances optical excitation at the nanometer length scale sufficient to optically detect surface-analyte interactions. A nanopore biosensor actively funnels and threads analytes through a molecular-scale aperture, wherein they are interrogated by electrical or optical means. Recently, solid-state plasmonic and nanopore structures have been integrated within monolithic devices that address fundamental challenges in each of the individual sensing methods and offer complimentary improvements in overall single-molecule sensitivity, detection rates, dwell time and scalability. Here, the physical phenomena and sensing principles of plasmonic and nanopore sensing are summarized to highlight the novel complementarity in dovetailing these techniques for vastly improved single-molecule sensing. A literature review of recent plasmonic nanopore devices is then presented to delineate methods for solid-state fabrication of a range of hybrid device formats, evaluate the progress and challenges in the detection of unlabeled and labeled analyte, and assess the impact and utility of localized plasmonic heating. Finally, future directions and applications inspired by the present state of the art are discussed.

The Pathway to Intelligence: Using Stimuli-Responsive Materials as Building Blocks for Constructing Smart and Functional Systems

Systems that are intelligent have the ability to sense their surroundings, analyze, and respond accordingly. In nature, many biological systems are considered intelligent (e.g., humans, animals, and cells). For man-made systems, artificial intelligence is achieved by massively sophisticated electronic machines (e.g., computers and robots operated by advanced algorithms). On the other hand, freestanding materials (i.e., not tethered to a power supply) are usually passive and static. Hence, herein, the question is asked: can materials be fabricated so that they are intelligent? One promising approach is to use stimuli-responsive materials; these "smart" materials use the energy supplied by a stimulus available from the surrounding for performing a corresponding action. After decades of research, many interesting stimuli-responsive materials that can sense and perform smart functions have been developed. Classes of functions discussed include practical functions (e.g., targeting and motion), regulatory functions (e.g., self-regulation and amplification), and analytical processing functions (e.g., memory and computing). The pathway toward creating truly intelligent materials can involve incorporating a combination of these different types of functions into a single integrated system by using stimuli-responsive materials as the basic building blocks.

Push-Button Method To Create Nanopores Using a Tesla-Coil Lighter

Controlled dielectric breakdown (CDB) of silicon nitride thin films immersed in electrolyte solution has been used to fabricate single nanofluidic channels with ∼10 nm and smaller diameters, nanopores, useful in single-molecule sensing and ionic circuit construction. A hand-held Tesla-coil lighter was used to form nanofluidic ionic conductors through a ∼10 nm thick silicon nitride membrane. Modifications to the conventional approach were required by the low-overhead Tesla-coil-assisted method (TCAM): increased circuit resistance by including water in place of electrolyte and discrete rather than continuous voltage applications. The resulting ionic conductance could be tuned with the number of voltage applications. TCAM and conventional CDB produced nanopores with different conductance versus pH curves, suggesting different surface chemistry. Nevertheless, sensing experiments using the canonical test molecule, λ-DNA, produced signals comparable to translocation results through solid-state nanopores fabricated by other methods. Thus, the TCAM method offers flexibility in fabrication and in the properties and function of the nanoscale ionic conductors that it can generate.

Properties of Omp2a-Based Supported Lipid Bilayers: Comparison with Polymeric Bioinspired Membranes

Omp2a β-barrel outer membrane protein has been reconstituted into supported lipid bilayers (SLBs) to compare the nanomechanical properties (elastic modulus, adhesion forces, and deformation) and functionality of the resulting bioinspired system with those of Omp2a-based polymeric nanomembranes (NMs). Protein reconstitution into lipid bilayers has been performed using different strategies, the most successful one consisting of a detergent-mediated process into preformed liposomes. The elastic modulus obtained for the lipid bilayer and Omp2a are ∼19 and 10.5 ± 1.7 MPa, respectively. Accordingly, the protein is softer than the lipid bilayer, whereas the latter exhibits less mechanical strength than polymeric NMs. Besides, the function of Omp2a in the SLB is similar to that observed for Omp2a-based polymeric NMs. Results open the door to hybrid bioinspired substrates based on the integration of Omp2a-proteoliposomes and nanoperforated polymeric freestanding NMs.

Nanoporous silicon nitride-based membranes of controlled pore size, shape and areal density: Fabrication as well as electrophoretic and molecular filtering characterization

A new route will be presented for an all-parallel fabrication of highly flexible, freestanding membranes with well-defined porosity. This fabrication is based on arrays of well-defined Au nanoparticles (NPs) exhibiting a high degree of hexagonal order as obtained in a first step by a proven micellar approach. These NP arrays serve as masks in a second reactive ion etching (RIE) step optimized for etching Si and some important Si compounds (silicon oxide, silicon nitride) on the nanoscale. Application to commercially available silicon nitride membranes of well-defined thickness, delivers a diaphragm with millions of nanopores of intended and controlled size, shape, and areal density with narrow distributions of these parameters. Electrophoretic transport measurements indicated a very low flow resistance of these porous membranes in ionic solutions as expected theoretically. Size-selective separation of protein molecules was demonstrated by real-time fluorescence microscopy.

Nanomaterial Preparation by Extrusion through Nanoporous Membranes

Template synthesis represents an important class of nanofabrication methods. Herein, recent advances in nanomaterial preparation by extrusion through nanoporous membranes that preserve the template membrane without sacrificing it, which is termed as "non-sacrificing template synthesis," are reviewed. First, the types of nanoporous membranes used in nanoporous membrane extrusion applications are introduced. Next, four common nanoporous membrane extrusion strategies: vesicle extrusion, membrane emulsification, precipitation extrusion, and biological membrane extrusion, are examined. These methods have been utilized to prepare a wide range of nanomaterials, including liposomes, emulsions, nanoparticles, nanofibers, and nanotubes. The principle and historical context of each specific technology are discussed, presenting prominent examples and evaluating their positive and negative features. Finally, the current challenges and future opportunities of nanoporous membrane extrusion methods are discussed.

Reversible Immobilization of Proteins in Sensors and Solid-State Nanopores

The controlled functionalization of surfaces with proteins is crucial for many analytical methods in life science research and biomedical applications. Here, a coating for silica-based surfaces is established which enables stable and selective immobilization of proteins with controlled orientation and tunable surface density. The coating is reusable, retains functionality upon long-term storage in air, and is applicable to surfaces of complex geometry. The protein anchoring method is validated on planar surfaces, and then a method is developed to measure the anchoring process in real time using silicon nitride solid-state nanopores. For surface attachment, polyhistidine tags that are site specifically introduced into recombinant proteins are exploited, and the yeast nucleoporin Nsp1 is used as model protein. Contrary to the commonly used covalent thiol chemistry, the anchoring of proteins via polyhistidine tag is reversible, permitting to take proteins off and replace them by other ones. Such switching in real time in experiments on individual nanopores is monitored using ion conductivity. Finally, it is demonstrated that silica and gold surfaces can be orthogonally functionalized to accommodate polyhistidine-tagged proteins on silica but prevent protein binding to gold, which extends the applicability of this surface functionalization method to even more complex sensor devices.

Bioinspired smart asymmetric nanochannel membranes

Bioinspired smart asymmetric nanochannel membranes (BSANM) have been explored extensively to achieve the delicate ionic transport functions comparable to those of living organisms. The abiotic system exhibits superior stability and robustness, allowing for promising applications in many fields. In view of the abundance of research concerning BSANM in the past decade, herein, we present a systematic overview of the development of the state-of-the-art BSANM system. The discussion is focused on the construction methodologies based on raw materials with diverse dimensions (i.e. 0D, 1D, 2D, and bulk). A generic strategy for the design and construction of the BSANM system is proposed first and put into context with recent developments from homogeneous to heterogeneous nanochannel membranes. Then, the basic properties of the BSANM are introduced including selectivity, gating, and rectification, which are associated with the particular chemical and physical structures. Moreover, we summarized the practical applications of BSANM in energy conversion, biochemical sensing and other areas. In the end, some personal opinions on the future development of the BSANM are briefly illustrated. This review covers most of the related literature reported since 2010 and is intended to build up a broad and deep knowledge base that can provide a solid information source for the scientific community.

Fabrication techniques enabling ultrathin nanostructured membranes for separations

The fabrication of nanostructured materials is an area of continuous improvement and innovative techniques that fulfill the demand of many fields of research and development. The continuously decreasing size of the smallest patternable feature has expanded the catalog of methods enabling the fabrication of nanostructured materials. Several of these nanofabrication techniques have sprouted from applications requiring nanoporous membranes such as molecular separations, cell culture, and plasmonics. This review summarizes methods that successfully produce through-pores in ultrathin films exhibiting an approximate pore size to thickness ratio of one, which has been shown to be beneficial due to high permeability and improved separation potential. The material reviewed includes large-area, parallel, and affordable approaches such as self-organizing polymers, nanosphere lithography, anodization, nanoimprint lithography as well as others such as solid phase crystallization and nanosphere lens lithography. The aim of this review is to provide a set of inexpensive fabrication techniques to produce nanostructured materials exhibiting pores ranging from 10 to 350 nm and a pore size to thickness ratio close to one. The fabrication methods described in this work have reported the successful manufacture of nanoporous membranes exhibiting the ideal characteristics to improve selectivity and permeability when applied as separation media in ultrafiltration.

Selective protein transport through ultra-thin suspended reduced graphene oxide nanopores

The nanoporous free-standing graphene membrane is of great interest in high performance separation technology. In particular, the separation of biological molecules with similar sizes is one of the key challenges in the purification of biomaterials. Here, we report a reliable, cost-effective, and facile method for the fabrication of a graphene-based nanosieve and its application in the separation of similar-size proteins. A suspended reduced graphene oxide (rGO) nanosieve with ultra-thin, large-area, well-ordered, and dense 15 nm-sized pores was fabricated using block copolymer (BCP) lithography. The fabricated 5 nm-ultrathin nanosieve with an area of 200 μm × 200 μm (an ultra-high aspect ratio of ∼40 000) endured pressure up to 1 atm, and effectively separated hemoglobin (Hb) from a mixture of hemoglobin and immunoglobulin G (IgG), the common proteins in human blood, in a highly selective and rapid manner. The use of the suspended rGO nanosieve is expected to provide a simple and manufacturable platform for practical biomolecule separation offering high selectivity and a large throughput.

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.

Electro-osmotic flow through nanopores in thin and ultrathin membranes

We theoretically study how the electro-osmotic fluid velocity in a charged cylindrical nanopore in a thin solid state membrane depends on the pore's geometry, membrane charge, and electrolyte concentration. We find that when the pore's length is comparable to its diameter, the velocity profile develops a concave shape with a minimum along the pore axis unlike the situation in very long nanopores with a maximum velocity along the central pore axis. This effect is attributed to the induced pressure along the nanopore axis due to the fluid flow expansion and contraction near the exit or entrance to the pore and to the reduction of electric field inside the nanopore. The induced pressure is maximal when the pore's length is about equal to its diameter while decreasing for both longer and shorter nanopores. A model for the fluid velocity incorporating these effects is developed and shown to be in a good agreement with numerically computed results.

Ultrathin Alumina Membranes as Scaffold for Epithelial Cell Culture from the Intestine of Rainbow Trout

Permeable membranes are indispensable for in vitro epithelial barrier models. However, currently available polymer-based membranes are low in porosity and relatively thick, resulting in a limited permeability and unrealistic culture conditions. In this study, we developed an ultrathin, nanoporous alumina membrane as novel cell culture interface for vertebrate cells, with focus on the rainbow trout (Onchorynchus mykiss) intestinal cell line RTgutGC. The new type of membrane is framed in a silicon chip for physical support and has a thickness of only 1 μm, with a porosity of 15% and homogeneous nanopores (Ø = 73 ± 21 nm). Permeability rates for small molecules, namely lucifer yellow, dextran 40, and bovine serum albumin, exceeded those of standard polyethylene terephthalate (PET) membranes by up to 27 fold. With the final goal to establish a representative model of the fish intestine for environmental toxicology, we engineered a simple culture setup, capable of testing the cellular response toward chemical exposure. Herein, cells were cultured in a monolayer on the alumina membranes and formed a polarized epithelium with apical expression of the tight junction protein ZO-1 within 14 days. Impedance spectroscopy, a noninvasive and real time electrical measurement, was used to determine cellular resistance during epithelial layer formation and chemical exposure to evaluate barrier functionality. Resistance values during epithelial development revealed different stages of epithelial maturity and were comparable with the in vivo situation. During chemical exposure, cellular resistance changed immediately when barrier tightness or cell viability was affected. Thus, our study demonstrates nanoporous alumina membranes as promising novel interface for alternative in vitro approaches, capable of allowing cell culture in a physiologically realistic manner and enabling high quality microscopy and sensitive measurement of cellular resistance.

Fabrication of "Plug and Play" Channels with Dual Responses by Host-Guest Interactions

The "Plug and Play" template can be individually or successively grafted by dual-responsive molecules on the α-CD modified channels by host-guest interactions and can be peeled off by UV irradiation. The artificial channels present six kinds of responses cycling among four states responding to three environment stimuli, as light, pH, and temperature.

Silicon Nitride Thin Films for Nanofluidic Device Fabrication

Silicon nitride is a ubiquitous and well-established nanofabrication material with a host of favourable properties for creating nanofluidic devices with a range of compelling designs that offer extraordinary discovery potential. Nanochannels formed between two thin silicon nitride windows can open up vistas for exploration by freeing transmission electron microscopy to interrogate static structures and structural dynamics in liquid-based samples. Nanopores present a strikingly different architecture—nanofluidic channels through a silicon nitride membrane—and are one of the most promising tools to emerge in biophysics and bioanalysis, offering outstanding capabilities for single molecule sensing. The constrained environments in such nanofluidic devices make surface chemistry a vital design and performance consideration. Silicon nitride has a rich and complex surface chemistry that, while too often formidable, can be tamed with new, robust surface functionalization approaches. We will explore how a simple structural element—a ∼100 nm-thick silicon nitride window—can be used to fabricate devices to wrest unprecedented insights from the nanoscale world. We will detail the intricacies of native silicon nitride surface chemistry, present surface chemical modification routes that leverage the richness of available surface moieties, and examine the effect of engineered chemical surface functionality on nanofluidic device character and performance.

Continuous high throughput nanofluidic separation through tangential-flow vertical nanoslit arrays

Nanofluidic devices exhibit unique, tunable transport properties that may lead to breakthroughs in molecular separations and sensing. However, the throughput of these devices is orders of magnitude too small for the processing of macroscopic samples. Here we overcome this problem by combining two technological innovations. First, nanofluidic channels are made as vertical slits connecting the two sides of a silicon nitride membrane. Arbitrary arrays of such nanoslits down to 15 nm wide with <6 Å uniformity were made by merging the idea of templating with chemical mechanical polishing to create a scalable, nanolithography-free wafer level process. Second, we provide for efficient solute transport to and from the openings of the nanoslits by incorporating the nanofluidic membrane into a microfluidic tangential-flow system, which is also fabricated at wafer level. As an exemplary application, we demonstrate charge-based continuous flow separation of small molecules with a selectivity of 100 and constant flux over more than 100 hours of operation. This proves the exciting possibility of exploiting transport phenomena governed by precision-engineered nanofluidic devices at a macroscopic scale.

Real-Time Profiling of Solid-State Nanopores During Solution-Phase Nanofabrication

We describe a method for simply characterizing the size and shape of a nanopore during solution-based fabrication and surface modification, using only low-overhead approaches native to conventional nanopore measurements. Solution-based nanopore fabrication methods are democratizing nanopore science by supplanting the traditional use of charged-particle microscopes for fabrication, but nanopore profiling has customarily depended on microscopic examination. Our approach exploits the dependence of nanopore conductance in solution on nanopore size, shape, and surface chemistry in order to characterize nanopores. Measurements of the changing nanopore conductance during formation by etching or deposition can be analyzed using our method to characterize the nascent nanopore size and shape, beyond the typical cylindrical approximation, in real-time. Our approach thus accords with ongoing efforts to broaden the accessibility of nanopore science from fabrication through use: it is compatible with conventional instrumentation and offers straightforward nanoscale characterization of the core tool of the field.