Particle Capture in Solid-State Multipores

Quad-Nanopore Array Enables High-Resolution Identification of Four Single-Stranded DNA Homopolymers

The solid-state nanopore technique holds the potential to develop mechanically stable and miniaturized DNA sequencing devices. However, the limited temporal resolution due to the high electric field inside the nanopore and the lack of an effective speed control strategy have hindered the realization of sequencing. Here, we reported a quad-array (four nanopores milled with ∼30 nm interpore spacing as a detection unit) that induced a redistribution of the electric field inside and outside the nanopore array and offered high-resolution discrimination of four ssDNA homopolymer types. We demonstrated that the quad-nanopore array well resolved the translocation events of polyA25 and had a length resolution of 20 nt. The molecular dynamic simulation confirmed the slowed-down translocations and superior performance of a quad-nanopore array. We found that the nanopore array configuration induced a direct reduction of the electric field inside the nanopore as well as an increase in the electrical field outside the nanopore due to electric field crosstalk. This dual benefit not only reduced the large driving force on DNA but also facilitated molecule capture through nanopores, therefore decreasing the voltage thresholds. Finally, the successful discrimination of four ssDNA homopolymer types (polyA25, polyT25, polyC25, and polyG10) was achieved using a voltage as low as 30 mV with a translocation speed of 8 μs/nt. These findings provide insights into nanopore arrays for discriminating short single-stranded nucleotides with high resolution and demonstrate promising potential for developing DNA sequencers that utilize nanopore arrays as sensing units.

Modulation of Ionic Current Rectification in Short Bipolar Nanopores

Bipolar nanopores, with asymmetric charge distributions, can induce significant ionic current rectification (ICR) at ultrashort lengths, finding potential applications in nanofluidic devices, energy conversion, and other related fields. Here, with simulations, we investigated the characteristics of ion transport and modulation of the ICR inside bipolar nanopores. With bipolar nanopores of half-positive and half-negative surfaces, the most significant ICR phenomenon appears at various concentrations. In these cases, the ICR ratios are independent of electrolyte types. In other cases where nanopores have oppositely charged surfaces of different lengths, ICR ratios are related to the mobility of anions and cations. The pore length and surface charge density can enhance ICR. As the pore length increases, ICR ratios first increase and then approach their saturation, which is determined by the surface charge density. External surface charges of nanopores can promote the ICR phenomenon mainly due to the enhancement of ion enrichment inside the nanopores by external surface conductance. The effective width of exterior charged surfaces under various conditions is also explored, which is inversely proportional to the pore length and salt concentration and linearly related to the pore diameter, surface charge density, and applied voltage. Our results may provide guidance for the design of bipolar porous membranes.

Scalability of nanopore osmotic energy conversion

Artificial nanofluidic networks are emerging systems for blue energy conversion that leverages surface charge-derived permselectivity to induce voltage from diffusive ion transport under salinity difference. Here the pivotal significance of electrostatic inter-channel couplings in multi-nanopore membranes, which impose constraints on porosity and subsequently influence the generation of large osmotic power outputs, is illustrated. Constructive interference is observed between two 20 nm nanopores of 30 nm spacing that renders enhanced permselectivity to osmotic power output via the recovered electroneutrality. On contrary, the interference is revealed as destructive in two-dimensional arrays causing significant deteriorations of the ion selectivity even for the nanopores sparsely distributed at an order of magnitude larger spacing than the Dukhin length. Most importantly, a scaling law is provided for deducing the maximal membrane area and porosity to avoid the selectivity loss via the inter-pore electrostatic coupling. As the electric crosstalk is inevitable in any fluidic network, the present findings can be a useful guide to design nanoporous membranes for scalable osmotic power generations.

Modulation mechanism of ionic transport through short nanopores by charged exterior surfaces

Short nanopores have various applications in biosensing, desalination, and energy conversion. Here, the modulation of ionic transport by charged exterior surfaces is investigated through simulations with sub-200 nm long nanopores under applied voltages. Detailed analysis of the ionic current, electric field strength, and fluid flow inside and outside nanopores reveals that charged exterior surfaces can increase ionic conductance by increasing both the concentration and migration speed of charge carriers. The electric double layers near charged exterior surfaces provide an ion pool and an additional passageway for counterions, which lead to enhanced exterior surface conductance and ionic concentrations at pore entrances and inside the nanopores. We also report that charges on the membrane surfaces increase the electric field strength inside nanopores. The effective width of a ring with surface charges placed at pore entrances (Lcs) is considered as well by studying the dependence of the current on Lcs. We find a linear relationship between the effective Lcs and the surface charge density and voltage, and an inverse relationship between the geometrical pore length and salt concentration. Our results elucidate the modulation mechanism of ionic transport through short nanopores by charged exterior surfaces, which is important for the design and fabrication of porous membranes.

Combining dynamic Monte Carlo with machine learning to study nanoparticle translocation

Resistive pulse sensing (RPS) measurements of nanoparticle translocation have the ability to provide information on single-particle level characteristics, such as diameter or mobility, as well as ensemble averages. However, interpreting these measurements is complex and requires an understanding of nanoparticle dynamics in confined spaces as well as the ways in which nanoparticles disrupt ion transport while inside a nanopore. Here, we combine Dynamic Monte Carlo (DMC) simulations with Machine Learning (ML) and Poisson-Nernst-Planck calculations to simultaneously simulate nanoparticle dynamics and ion transport during hundreds of independent particle translocations as a function of nanoparticle size, electrophoretic mobility, and nanopore length. The use of DMC simulations allowed us to explicitly investigate the effects of Brownian motion and nanoparticle/nanopore characteristics on the amplitude and duration of translocation signals. Simulation results were verified with experimental RPS measurements and found to be in quantitative agreement.

Quasi-Stable Salt Gradient and Resistive Switching in Solid-State Nanopores

Understanding and control of ion transport in a fluidic channel is of crucial importance for iontronics. The present study reports on quasi-stable ionic current characteristics in a SiN_x nanopore under a salinity gradient. An intriguing interplay between electro-osmotic flow and local ion density distributions in a solid-state pore is found to induce highly asymmetric ion transport to negative differential resistance behavior under a 100-fold difference in the cross-membrane salt concentrations. Meanwhile, a subtle change in the salinity gradient profile led to observations of resistive switching. This peculiar characteristic was suggested to stem from quasi-stable local ion density around the channel that can be switched between two distinct states via the electro-osmotic flow under voltage control. The present findings may be useful for neuromorphic devices based on micro- and nanofluidic channels.

Individually Addressable Multi-nanopores for Single-Molecule Targeted Operations

The fine-tuning of molecular transport is a ubiquitous problem of single-molecule methods. The latter is evident even in powerful single-molecule techniques such as nanopore sensing, where the quest for resolving more detailed biomolecular features is often limited by insufficient control of the dynamics of individual molecules within the detection volume of the nanopore. In this work, we introduce and characterize a reconfigurable multi-nanopore architecture that enables additional channels to manipulate the dynamics of DNA molecules in a nanopore. We show that the fabrication process of this device, consisting of four adjacent, individually addressable nanopores located at the tip of a quartz nanopipette, is fast and highly reproducible. By individually tuning the electric field across each nanopore, these devices can operate in several unique cooperative detection modes that allow moving, sensing, and trapping of DNA molecules with high efficiency and increased temporal resolution.

High-throughput single nanoparticle detection using a feed-through channel-integrated nanopore

The outstanding sensitivity of solid-state nanopore sensors comes at a price of low detection efficiency due to the lack of active means to transfer objects into the nanoscale sensing zone. Here we report on a key technology for high-throughput single-nanoparticle detection which exploits mutual effects of microfluidics control and multipore electrophoresis in nanopore-in-channel units integrated on a thin Si₃N₄ membrane. Using this novel nanostructure, we demonstrated a proof-of-concept for influenza viruses via hydropressure regulation of mass transport in the fluidic channel for continuous feeding of biosamples into the effective electric field extending out from the nanopores, wherein the feed-through mechanism allowed us to selectively detect charged objects in physiological media such as human saliva. With the versatility of nanopore sensing technologies applicable to analytes of virtually any size from cells to polynucleotides, the present integration strategy may open new avenues for practical ultrasensitive bioanalytical tools.

High-throughput single-particle detections using a dual-height-channel-integrated pore

We report a proof-of-principle demonstration of particle concentration to achieve high-throughput resistive pulse detections of bacteria using a microfluidic-channel-integrated micropore. We fabricated polymeric nanochannels to trap micrometer-sized bioparticles via a simple water pumping mechanism that allowed aggregation-free size-selective particle concentration with negligible loss. Single-bioparticle detections by ionic current measurements were then implemented through releasing and transporting the thus-collected analytes to the micropore. As a result, we attained two orders of magnitude enhancement in the detection throughput by virtue of an accumulation effect via hydrodynamic control. The device concept presented may be useful in developing nanopores and nanochannels for high-throughput single-particle and -molecule analyses.