Unraveling Clinical Glycoproteome by Integrating Affinity Enrichment with Nanopore Sequencing.

This prospect explores the integration of enrichment strategies with nanopore detection to advance clinical glycoproteomics. Glycoproteins, crucial for understanding biological processes, pose challenges due to their low abundance and structural diversity. Enrichment techniques using lectin affinity, boronate affinity, and hydrazide chemistry and especially molecular imprinted polymers may selectively and specifically isolate glycoproteins from complex samples, while nanopore technology enables label-free, real-time, and single-molecule analysis. This approach holds promise for disease-related glycosylation studies, biomarker discovery, personalized medicine, and streamlined clinical analysis. Standardization, optimization, and data analysis remain challenges, requiring interdisciplinary collaborations and technological advancements. Overall, this integration may offer transformative potential for clinical glycoproteomics and innovative diagnostic and therapeutic strategies.

Synaptic Response of Fluidic Nanopores: The Connection of Potentiation with Hysteresis.

Iontronic fluidic ionic/electronic components are emerging as promising elements for artificial brain-like computation systems. Nanopore ionic rectifiers can be operated as a synapse element, exhibiting conductance modulation in response to a train of voltage impulses, thus producing programmable resistive states. We propose a model that replicates hysteresis, rectification, and time domain response properties, based on conductance modulation between two conducting modes and a relaxation time of the state variable. We show that the kinetic effects observed in hysteresis loops govern the potentiation phenomena related to conductivity modulation. To illustrate the efficacy of the model, we apply it to replicate rectification, hysteresis and conductance modulation of two different experimental systems: a polymer membrane with conical pores, and a blind-hole nanoporous anodic alumina membrane with a barrier oxide layer. We show that the time transient analysis of the model develops the observed potentiation and depression phenomena of the synaptic properties.

Tailored Fabrication of 3D Nanopores Made of Dielectric Oxides for Multiple Nanoscale Applications.

Solid-state nanopores are a key platform for single-molecule detection and analysis that allow engineering of their properties by controlling size, shape, and chemical functionalization. However, approaches relying on polymers have limits for what concerns hardness, robustness, durability, and refractive index. Nanopores made of oxides with high dielectric constant would overcome such limits and have the potential to extend the suitability of solid-state nanopores toward optoelectronic technologies. Here, we present a versatile method to fabricate three-dimensional nanopores made of different dielectric oxides with convex, straight, and concave shapes and demonstrate their functionality in a series of technologies and applications such as ionic nanochannels, ionic current rectification, memristors, and DNA sensing. Our experimental data are supported by numerical simulations that showcase the effect of different shapes and oxide materials. This approach toward robust and tunable solid-state nanopores can be extended to other 3D shapes and a variety of dielectrics.

Parametrically guided design of beta barrels and transmembrane nanopores using deep learning.

Francis Crick's global parameterization of coiled coil geometry has been widely useful for guiding design of new protein structures and functions. However, design guided by similar global parameterization of beta barrel structures has been less successful, likely due to the deviations required from ideal beta barrel geometry to maintain extensive inter-strand hydrogen bonding without introducing considerable backbone strain. Instead, beta barrels and other protein folds have been designed guided by 2D structural blueprints; while this approach has successfully generated new fluorescent proteins, transmembrane nanopores, and other structures, it requires considerable expert knowledge and provides only indirect control over the global barrel shape. Here we show that the simplicity and control over shape and structure provided by global parametric representations can be generalized beyond coiled coils by taking advantage of the rich sequence-structure relationships implicit in RoseTTAFold based inpainting and diffusion design methods. Starting from parametrically generated idealized barrel backbones, both RFjoint inpainting and RFdiffusion readily incorporate the backbone irregularities necessary for proper folding with minimal deviation from the idealized barrel geometries. We show that for beta barrels across a broad range of global beta sheet parameterizations, these methods achieve high in silico and experimental success rates, with atomic accuracy confirmed by an X-ray crystal structure of a novel beta barrel topology, and de novo designed 12, 14, and 16 stranded transmembrane nanopores with conductances ranging from 200 to 500 pS. By combining the simplicity and control of parametric generation with the high success rates of deep learning based protein design methods, our approach makes the design of proteins where global shape confers function, such as beta barrel nanopores, more precisely specifiable and accessible.

Analysis of structural defects and their influence on red-emitting γ-Al2O3:Mn4+,Mg2+ nanowires using positron annihilation spectroscopy.

The present paper reported on the analysis of structural defects and their influence on the red-emitting γ-Al2O3:Mn4+,Mg2+ nanowires using positron annihilation spectroscopy (PAS). The nanowires were synthesized by hydrothermal method and low-temperature post-treatment using glucose as a reducing agent. X-ray diffraction (XRD), scanning electron microscopy (SEM), photoluminescence (PL), and photoluminescence excitation (PLE) were utilized, respectively, for determining the structural phase, morphology and red-emitting intensity in studied samples. Three PAS experiments, namely, positron annihilation lifetime (PAL), Doppler broadening (DB), and electron momentum distribution (EMD), were simultaneously performed to investigate the formations of structural defects in synthesized materials. Obtained results indicated that the doping concentration of 0.06% was optimal for the substitution of Mn4+ and Mg2+ to two Al3+ sites and the formation of oxygen vacancy (VO)-rich vacancy clusters (2VAl + 3VO) and large voids (~0.7 nm) with less Al atoms. Those characteristics reduced the energy transfer between Mn4+ ions, thus consequently enhanced the PL and PLE intensities. Moreover, this optimal doping concentration also effectively controlled the size of nanopores (~2.18 nm); hence, it is expected to maintain the high thermal conductivity of γ-Al2O3 nanowire-phosphor. The present study, therefore, demonstrated a potential application of γ-Al2O3 nanowire-phosphor in fabricating the high-performance optoelectronic devices.

Light-Driven Ionic and Molecular Transport through Atomically Thin Single Nanopores in MoS2/WS2 Heterobilayers.

Nanofluidic ionic and molecular transport through atomically thin nanopore membranes attracts broad research interest from both scientific and industrial communities for environmental, healthcare, and energy-related technologies. To mimic the biological ion pumping functions, recently, light-induced and quantum effect-facilitated charge separation in heterogeneous 2D-material assemblies is proposed as the fourth type of driving force to achieve active and noninvasive transport of ionic species through synthetic membrane materials. However, to date, engineering versatile van der Waals heterostructures into 2D nanopore membranes remains largely unexplored. Herein, we fabricate single nanopores in heterobilayer transition metal dichalcogenide membranes with helium ion beam irradiation and demonstrate the light-driven ionic transport and molecular translocation phenomena through the atomically thin nanopores. Experimental and simulation results further elucidate the driving mechanism as the photoinduced near-pore electric potential difference due to type II band alignment of the semiconducting WS2 and MoS2 monolayers. The strength of the photoinduced localized electric field near the pore region can be approximately 1.5 times stronger than that of its counterpart under the conventional voltage-driven mode. Consequently, the light-driven mode offers better spatial resolution for single-molecule detection. Light-driven ionic and molecular transport through nanopores in van der Waals heterojunction membranes anticipates transformative working principles for next-generation biomolecular sequencing and gives rise to fascinating opportunities for light-to-chemical energy harvesting nanosystems.

Performance of single nanopore and multi-pore membranes for blue energy.

The salinity gradient power extracted from the mixing of electrolyte solutions at dierent concentrations through selective nanoporous membranes is a promising route to renewable energy. However, several challenges need to be addressed to make this technology protable, one of the most relevant being the increase of the extractable power per membrane area. Here, the performance of asymmetric conical and bullet-shaped nanopores in a 50 nm thick membrane are studied via electrohydrodynamic simulations, varying the pore radius, curvature, and surface charge. The output power reaches ∼ 60 pW per pore for positively charged membranes (surface charge σw =160 mC/m2 ) and ∼ 30 pW for negatively charges ones, σw =-160 mC/m2 and it is robust to minor variations of nanopore shape and radius. A theoretical argument that takes into account the interaction among neighbour pores allows to extrapolate the single-pore performance to multi-pore membranes showing that power densities from tens to hundreds of W/m2 can be reached by proper tuning of the nanopore number density and the boundary layer thickness. Our model for scaling single-pore performance to multi-pore membrane can be applied also to experimental data providing a simple tool to effectively compare different nanopore membranes in blue energy applications.

Enhanced magnetism derived from pore-edge spins in thin Fe3GeTe2nanomeshes.

The growth of two-dimensional van der Waals magnetic materials presents attractive opportunities for exploring new physical phenomena and valuable applications. Among these materials, Fe3GeTe2(FGT) exhibits a variety of remarkable properties and has garnered significant attention. Herein, we have for the first time created a nanomesh structure-a honeycomb-like array of hexagonal nanopores-with the zigzag pore-edge atomic structure on thin FGT flakes with and without oxidation of the pore edges. It is revealed that the magnitude of ferromagnetism (FM) significantly increases in both samples compared with bulk flakes without nanomeshes. Critical temperature annealing results in the formation of zigzag pore edges and interpore zigzag-edge nanoribbons. We unveil that the non-oxide (O) termination of the Fe dangling bonds on these zigzag edges enhances FM behavior, while O-termination suppresses this FM by introducing antiferromagnetic behavior through edge O-Fe coupling. FGT nanomeshes hold promise for the creation of strong FM and their effective application in magnetic and spintronic systems.

Understanding the Wettability of C1N1 (Sub)Nanopores: Implications for Porous Carbonaceous Electrodes.

Understanding how water interacts with nanopores of carbonaceous electrodes is crucial for energy storage and conversion applications. A high surface area of carbonaceous materials does not necessarily need to translate to a high electrolyte-solid interface area. Herein, we study the interaction of water with nanoporous C1N1 materials to explain their very low specific capacity in aqueous electrolytes despite their high surface area. Water was used to probe chemical environments, provided by pores of different sizes, in 1H MAS NMR experiments. We observe that regardless of their high hydrophilicity, only a negligible portion of water can enter the nanopores of C1N1, in contrast to a reference pure carbon material with a similar pore structure. The common paradigm that water easily enters hydrophilic pores does not apply to C1N1 nanopores below a few nanometers. Calorimetric and sorption experiments demonstrated strong water adsorption on the C1N1 surface, which restricts water mobility across the interface and impedes its penetration into the nanopores.

Compliant DNA Origami Nanoactuators as Size-Selective Nanopores.

Biological nanopores crucially control the import and export of biomolecules across lipid membranes in cells. They have found widespread use in biophysics and biotechnology, where their typically narrow, fixed diameters enable selective transport of ions and small molecules, as well as DNA and peptides for sequencing applications. Yet, due to their small channel sizes, they preclude the passage of large macromolecules, e.g., therapeutics. Here, the unique combined properties of DNA origami nanotechnology, machine-inspired design, and synthetic biology are harnessed, to present a structurally reconfigurable DNA origami MechanoPore (MP) that features a lumen that is tuneable in size through molecular triggers. Controllable switching of MPs between 3 stable states is confirmed by 3D-DNA-PAINT super-resolution imaging and through dye-influx assays, after reconstitution of the large MPs in the membrane of liposomes via an inverted-emulsion cDICE technique. Confocal imaging of transmembrane transport shows size-selective behavior with adjustable thresholds. Importantly, the conformational changes are fully reversible, attesting to the robust mechanical switching that overcomes pressure from the surrounding lipid molecules. These MPs advance nanopore technology, offering functional nanostructures that can be tuned on-demand - thereby impacting fields as diverse as drug delivery, biomolecule sorting, and sensing, as well as bottom-up synthetic biology.

Real-Time Measurement of a Weak Interaction of a Transcription Factor Motif with a Protein Hub at Single-Molecule Precision.

Transcription factors often interact with other protein cofactors, regulating gene expression. Direct detection of these brief events using existing technologies remains challenging due to their transient nature. In addition, intrinsically disordered domains, intranuclear location, and lack of cofactor-dependent active sites of transcription factors further complicate the quantitative analysis of these critical processes. Here, we create a genetically encoded label-free sensor to identify the interaction between a motif of the MYC transcription factor, a primary cancer driver, and WDR5, a chromatin-associated protein hub. Using an engineered nanopore equipped with this motif, WDR5 is probed through reversible captures and releases in a one-by-one and time-resolved fashion. Our single-molecule kinetic measurements indicate a weak-affinity interaction arising from a relatively slow complex association and a fast dissociation of WDR5 from the tethered motif. Further, we validate this subtle interaction by determinations in an ensemble using single nanodisc-wrapped nanopores immobilized on a biolayer interferometry sensor. This study also provides the proof-of-concept for a sensor that reveals unique recognition signatures of different protein binding sites. Our foundational work may be further developed to produce sensing elements for analytical proteomics and cancer nanomedicine.

A Robust Parallel Computing Data Extraction Framework for Nanopore Experiments.

The success of a nanopore experiment relies not only on the quality of the experimental design but also on the performance of the analysis program utilized to decipher the ionic perturbations necessary for understanding the fundamental molecular intricacies. An event extraction framework is developed that leverages parallel computing, efficient memory management, and vectorization, yielding significant performance enhancement. The newly developed abf-ultra-simple function extracts key parameters from the header critical for the operation of open-seek-read-close data loading architecture running on multiple cores. This underpins the swift analysis of large files where an ≈ × 18 improvement is found for a 100 min-long file (≈4.5 GB) compared to the more traditional single (cell) array data loading method. The application is benchmarked against five other analysis platforms showcasing significant performance enhancement (>2 ×-1120 ×). The integrated provisions for batch analysis enable concurrently analyzing multiple files (vital for high-bandwidth experiments). Furthermore, the application is equipped with multi-level data fitting based on abrupt changes in the event waveform. The application condenses the extracted events to a single binary file improving data portability (e.g., 16 GB file with 28 182 events reduces to 47.9 MB-343 × size reduction) and enables a multitude of post-analysis extractions to be done efficiently.

Study on Mechanical Properties of Nanopores in CoCrFeMnNi High-Entropy Alloy Used as Drug-Eluting Stent.

The CoCrFeMnNi high-entropy alloy is commonly used for vascular stents due to its excellent mechanical support and ductility. However, as high-entropy alloy stents can cause inflammation in the blood vessels, leading to their re-narrowing, drug-eluting stents have been developed. These stents have nanopores on their surfaces that can carry drug particles to inhibit inflammation and effectively prevent re-narrowing of the blood vessels. To optimize the mechanical properties and drug-carrying capacity of high-entropy alloy stents, a high-entropy alloy system with different wide and deep square-shaped nanopore distributions is created using molecular dynamics. The mechanical characteristics and dislocation evolution mechanism of different nanopore high-entropy alloy systems under tensile stress were studied. The results showed that the CoCrFeMnNi high-entropy alloy with a rational nanopore distribution can effectively maintain the mechanical support required for a vascular stent. This research provides a new direction for the manufacturing process of nanopores on the surfaces of high-entropy alloy stents.

Detection of aldehydes from degradation of lipid nanoparticle formulations using a hierarchically-organized nanopore electrochemical biosensor.

Degradation of ionizable lipids in mRNA-based vaccines was recently found to deactivate the payload, demanding rigorous monitoring of impurities in lipid nanoparticle (LNP) formulations. However, parallel screening for lipid degradation in customized delivery systems for next-generation therapeutics maintains a challenging and unsolved problem. Here, we describe a nanopore electrochemical sensor to detect ppb-levels of aldehydes arising from lipid degradation in LNP formulations that can be deployed in massively parallel fashion. Specifically, we combine nanopore electrodes with a block copolymer (BCP) membrane capable of hydrophobic gating of analyte transport between the bulk solution and the nanopore volume. By incorporating aldehyde dehydrogenase (ALDH), enzymatic oxidation of aldehydes generates NADH to enable ultrasensitive voltammetric detection with limits-of-detection (LOD) down to 1.2 ppb. Sensor utility was demonstrated by detecting degradation of N-oxidized SM-102, the ionizable lipid in Moderna's SpikeVax™ vaccine, in mRNA-1273 LNP formulation. This work should be of significant use in the pharmaceutical industry, paving the way for automated on-line quality assessments of next-generation therapeutics.

Enhanced Nanoparticle Sensing in a Highly Viscous Nanopore.

Slowing down translocation dynamics is a crucial challenge in nanopore sensing of small molecules and particles. Here, it is reported on nanoparticle motion-mediated local viscosity enhancement of water-organic mixtures in a nanofluidic channel that enables slow translocation speed, enhanced capture efficiency, and improved signal-to-noise ratio by transmembrane voltage control. It is found that higher detection rates of nanoparticles under larger electrophoretic voltage in the highly viscous solvents. Meanwhile, the strongly pulled particles distort the liquid in the pore at high shear rates over 103 s-1 which leads to a counterintuitive phenomenon of slower translocation speed under higher voltage via the induced dilatant viscosity behavior. This mechanism is demonstrated as feasible with a variety of organic molecules, including glycerol, xanthan gum, and polyethylene glycol. The present findings can be useful in resistive pulse analyses of nanoscale objects such as viruses and proteins by allowing a simple and effective way for translocation slowdown, improved detection throughput, and enhanced signal-to-noise ratio.

Nanopore Blockade Sensors for Quantitative Analysis Using an Optical Nanopore Assay.

Nanopore sensing is a popular biosensing strategy that is being explored for the quantitative analysis of biomarkers. With low concentrations of analytes, nanopore sensors face challenges related to slow response times and selectivity. Here, we demonstrate an approach to rapidly detect species at ultralow concentrations using an optical nanopore blockade sensor for quantitative detection of the protein vascular endothelial growth factor (VEGF). This sensor relies on monitoring fluorescent polystyrene nanoparticles blocking nanopores in a nanopore array of 676 nanopores. The fluorescent signal is read out using a wide-field fluorescence microscope. Nonspecific blockade events are then distinguished from specific blockade events based on the ability to pull the particles out of the pore using an applied electric field. This allows the detection of VEGF at sub-picomolar concentration in less than 15 min.

High Volumetric Energy Density Supercapacitor of Additive-Free Quantum Dot Hierarchical Nanopore Structure.

The high surface-area-to-volume ratio of colloidal quantum dots (QDs) positions them as promising materials for high-performance supercapacitor electrodes. However, the challenge lies in achieving a highly accessible surface area, while maintaining good electrical conductivity. An efficient supercapacitor demands a dense yet highly porous structure that facilitates efficient ion-surface interactions and supports fast charge mobility. Here we demonstrate the successful development of additive-free ultrahigh energy density electric double-layer capacitors based on quantum dot hierarchical nanopore (QDHN) structures. Lead sulfide QDs are assembled into QDHN structures that strike a balance between electrical conductivity and efficient ion diffusion by employing meticulous control over inter-QD distances without any additives. Using ionic liquid as the electrolyte, the high-voltage ultrathin-film microsupercapacitors achieve a remarkable combination of volumetric energy density (95.6 mWh cm-3) and power density (13.5 W cm-3). This achievement is attributed to the intrinsic capability of QDHN structures to accumulate charge carriers efficiently. These findings introduce innovative concepts for leveraging colloidal nanomaterials in the advancement of high-performance energy storage devices.

Trapping and recapturing single DNA molecules with pore-cavity-pore device.

Single-molecule detection technology is a technique capable of detecting molecules at the single-molecule level, characterized by high sensitivity, high resolution, and high specificity. Nanopore technology, as one of the single-molecule detection tools, is widely used to study the structure and function of biomolecules. In this study, we constructed a small-sized nanopore with a pore-cavity-pore structure, which can achieve a higher reverse capture rate. Through simulation, we investigated the electrical potential distribution of the nanopore with a pore-cavity-pore structure and analyzed the influence of pore size on the potential distribution. Accordingly, different pore sizes can be designed based on the radius of gyration of the target biomolecules, restricting their escape paths inside the chamber. In the future, nanopores with a pore-cavity-pore structure based on two-dimensional thin film materials are expected to be applied in single-molecule detection research, which provides new insights for various detection needs.

Influence of the Dielectric Constant on the Ionic Current Rectification of Bipolar Nanopores.

In this paper, we investigate how the dielectric constant, ϵ, of an electrolyte solvent influences the current rectification characteristics of bipolar nanopores. It is well recognized that bipolar nanopores with two oppositely charged regions rectify current when exposed to an alternating electric potential difference. Here, we consider dilute electrolytes with NaCl only and with a mixture of NaCl and charged nanoparticles. These systems are studied using two levels of description, all-atom explicit water molecular dynamics (MD) simulations and coarse-grained implicit solvent MD simulations. The charge density and electric potential profiles and current-voltage relationship predicted by the implicit solvent simulations with ϵ = 11.3 show good agreement with the predictions from the explicit water simulations. Under nonequilibrium conditions, the predictions of the implicit solvent simulations with a dielectric constant closer to the one of bulk water are significantly different from the predictions obtained with the explicit water model. These findings are closely aligned with experimental data on the dielectric constant of water when confined to nanometric spaces, which suggests that ϵ decreases significantly compared to its value in the bulk. Moreover, the largest electric current rectification is observed in systems containing nanoparticles when ϵ = 78.8. Using enhanced sampling, we have shown that this larger rectification arises from the presence of a significantly deeper minimum in the free energy of the system with a larger ϵ, and when a negative voltage bias is applied. Since implicit solvent models and mean-field continuum theories are often used to design Janus membranes based on bipolar nanopores, this work highlights the importance of properly accounting for the effects of confinement on the dielectric constant of the electrolyte solvent. The results presented here indicate that the dielectric constant in implicit solvent simulations may be used as an adjustable parameter to approximately account for the effects of nanometric confinement on aqueous electrolyte solvents.

Advances in Two-Dimensional Ion-Selective Membranes: Bridging Nanoscale Insights to Industrial-Scale Salinity Gradient Energy Harvesting.

Salinity gradient energy, often referred to as the Gibbs free energy difference between saltwater and freshwater, is recognized as "blue energy" due to its inherent cleanliness, renewability, and continuous availability. Reverse electrodialysis (RED), relying on ion-selective membranes, stands as one of the most prevalent and promising methods for harnessing salinity gradient energy to generate electricity. Nevertheless, conventional RED membranes face challenges such as insufficient ion selectivity and transport rates and the difficulty of achieving the minimum commercial energy density threshold of 5 W/m2. In contrast, two-dimensional nanostructured materials, featuring nanoscale channels and abundant functional groups, offer a breakthrough by facilitating rapid ion transport and heightened selectivity. This comprehensive review delves into the mechanisms of osmotic power generation within a single nanopore and nanochannel, exploring optimal nanopore dimensions and nanochannel lengths. We subsequently examine the current landscape of power generation using two-dimensional nanostructured materials in laboratory-scale settings across various test areas. Furthermore, we address the notable decline in power density observed as test areas expand and propose essential criteria for the industrialization of two-dimensional ion-selective membranes. The review concludes with a forward-looking perspective, outlining future research directions, including scalable membrane fabrication, enhanced environmental adaptability, and integration into multiple industries. This review aims to bridge the gap between previous laboratory-scale investigations of two-dimensional ion-selective membranes in salinity gradient energy conversion and their potential large-scale industrial applications.