SiNx Membrane Research Articles

Fast Fabrication of Solid-State Nanopores for DNA Molecule Analysis.

Solid-state nanopores have been developed as a prominent tool for single molecule analysis in versatile applications. Although controlled dielectric breakdown (CDB) is the most accessible method for a single nanopore fabrication, it is still necessary to improve the fabrication efficiency and avoid the generation of multiple nanopores. In this work, we treated the SiNx membranes in the air–plasma before the CDB process, which shortened the time-to-pore-formation by orders of magnitude. λ-DNA translocation experiments validated the functionality of the pore and substantiated the presence of only a single pore on the membrane. Our fabricated pore could also be successfully used to detect short single-stranded DNA (ssDNA) fragments. Using to ionic current signals, ssDNA fragments with different lengths could be clearly distinguished. These results will provide a valuable reference for the nanopore fabrication and DNA analysis.

Understanding Electrical Conduction and Nanopore Formation During Controlled Breakdown.

Controlled breakdown has recently emerged as a highly appealing technique to fabricate solid-state nanopores for a wide range of biosensing applications. This technique relies on applying an electric field of approximately 0.4-1 V nm-1 across the membrane to induce a current, and eventually, breakdown of the dielectric. Although previous studies have performed controlled breakdown under a range of different conditions, the mechanism of conduction and breakdown has not been fully explored. Here, electrical conduction and nanopore formation in SiNx membranes during controlled breakdown is studied. It is demonstrated that for Si-rich SiNx , oxidation reactions that occur at the membrane-electrolyte interface limit conduction across the dielectric. However, for stoichiometric Si3 N4 the effect of oxidation reactions becomes relatively small and conduction is predominately limited by charge transport across the dielectric. Several important implications resulting from understanding this process are provided which will aid in further developing controlled breakdown in the coming years, particularly for extending this technique to integrate nanopores with on-chip nanostructures.

Numerical modeling of in-plane thermal conductivity measurement methods based on a suspended membrane setup

A numerical modeling study, based on 3D finite element method (FEM) simulation and 1D analytical solutions, has been carried out to evaluate the capabilities of two ac methods for measuring in-plane thermal conductivity of thin film deposited on the back of a suspended SiNx membrane setup. Two parallel metal strips are present on the top of the dielectric membrane. One strip (S1) serves as both heater and thermometer, while another one (S2) acts as thermometer only. For a modified phase shift (MPS) method, it is crucial to extract the in-plane thermal diffusivity from the phase shift of the temperature oscillation on S2. It was found that the frequency window for carrying out the data fitting became narrower as the in-plane thermal diffusivity of the composite membrane (α∥,C) increased, primarily due to the failure of the semi-infinite width assumption in the low frequency region. To ensure the validity of the method, the upper limit of α∥,C should not exceed ~1.8 × 10−5 m2s−1 for the specific membrane dimension under consideration (1 × 1 mm2). On the other hand, inspired by a modified Ångström method proposed by Zhu recently, we suggest a new data reduction methodology which takes advantage of the phase shift on both S1 and S2 as well as the amplitude on S1. Based on the simulation results, it is expected that the non-ideality associated with the three “observables” may be at least partially canceled out. Therefore, the frequency window selection for carrying out the data fitting is not sensitive to the magnitude of α∥,C and the upper limit of measurable αC,∥ can be further increased with respect to the MPS method. For typical specimen films whose in-plane thermal conductivity ranges from 0.84 W m−1K−1 to 50 W m−1K−1, the method proposed here yields a theoretical measurement uncertainty of less than 5%.

Mapping and Controlling Liquid Layer Thickness in Liquid-Phase (Scanning) Transmission Electron Microscopy.

Liquid-Phase (Scanning) Transmission Electron Microscopy (LP-(S)TEM) has become an essential technique to monitor nanoscale materials processes in liquids in real-time. Due to the pressure difference between the liquid and the microscope vacuum, bending of the silicon nitride (SiNx ) membrane windows generally occurs. This causes a spatially varying liquid layer thickness that makes interpretation of LP-(S)TEM results difficult due to a locally varying achievable resolution and diffusion limitations. To mediate these difficulties, it is shown: 1) how to quantitatively map liquid layer thickness for any liquid at less than0.01 e- Å-2 total dose; 2) how to dynamically modulate the liquid thickness by tuning the internal pressure in the liquid cell, co-determined by the Laplace pressure and the external pressure. It is demonstrated that reproducible inward bulging of the window membranes can be realized, leading to an ultra-thin liquid layer in the central window area for high-resolution imaging. Furthermore, it is shown that the liquid thickness can be dynamically altered in a programmed way, thereby potentially overcoming the diffusion limitations towards achieving bulk solution conditions. The presented approaches provide essential ways to measure and dynamically adjust liquid thickness in LP-(S)TEM experiments, enabling new experiment designs and better control of solution chemistry.

Combining quantitative ADF STEM with SiNx membrane-based MEMS devices: A simulation study with Pt nanoparticles

Computer simulations are used to assess the influence of a 20-nm-thick SiNx membrane on the quantification of atomic-resolution annular dark-field (ADF) scanning transmission electron microscopy images of Pt nanoparticles. The discussions include the effect of different nanoparticle/membrane arrangements, accelerating voltage, nanoparticle thickness and the presence of adjacent atomic columns on the accuracy with which the number of Pt atoms in each atom column can be counted. The results, which are based on the use of ADF scattering cross-sections, show that an accuracy of better than a single atom is attainable at 200 and 300 kV. At 80kV, the scattering in a typical SiNx membrane is sufficiently strong that the best possible atom counting accuracy is reduced to +/- 2 atoms. The implications of the work for quantitative studies of Pt nanoparticles imaged through SiNx membranes are discussed.

Fabricating Ultra-thin Silicon Nitride Membranes Suspended on Silicon Wafer

Ultrathin silicon nitride SiNx membrane suspended on a silicon wafer is a popular two-dimensional platform in MEMS applications. The unsupported membrane has a low thermal conductivity, is electrically insulated, and very robust against mechanical impact. Remarkably thin, it is difficult to fabricate and manipulate. Recently equipped with a dual chamber system for plasma enhanced chemical vapor deposition (PECVD) and reactive ion etching, we calibrate it to deposit silicon nitride Si3N4, silicon dioxide SiO2, and to dry etch these materials. Based on the superb quality of Si3N4, we perform a through-wafer etch that creates suspended Si3N4 membranes. The recipe is reliable and reproducible. We analyze the membrane’s chemical composition and optical properties. Although created by PECVD, the membrane is so robust that it survives multiple lithography steps. It extends our capability to study thermal transport at the submicron scale as well as to fabricate micron size devices for MEMS applicati

Dielectric Coatings for Resistive Pulse Sensing Using Solid-State Pores.

The present study reports on the systematic characterization of the effectiveness of dielectric coating to tailor capture-to-translocation dynamics of single particles in solid-state pores. We covered the surface of SiNx membranes with SiO2, HfO2, Al2O3, TiO2, or ZnO, which allowed us to change the ζ-potential at the pore wall, reflecting the isoelectric points of these coating materials. Resistive pulse measurements of negatively charged polystyrene beads elucidated more facile electrophoretic capture of the particles and slower translocation motions in the channel under more negative electric potential at the oxide surface. These findings provide a guide to engineer pore wall surface for optimizing the translocation dynamics for efficient sensing of particles and molecules.

Chemically-Tuned Solid-State Nanopores for Single-Molecule Biophyics

Solid-state nanopores (SSNs) are nanofluidic conduits fabricated through synthetic materials such as silicon nitride, silicon dioxide, graphene, etc. Intrapore variations, temporal fluctuations in open-pore current and analyte sticking are legacy limitations associated with SSNs which have challenged its footprint in single molecule science. We report a modification to the Controlled Dielectric Breakdown (CDB) method of nanopore fabrication on silicon nitride (SiNx) membranes where a blend of electrolyte and sodium hypochlorite is used as the conducting solution. These chemically tuned SSNs are devoid of the fundamental challenges associated with SSNs. The change in surface chemistry, with ∼3 orders of magnitude weaker Ka compared to conventional CDB nanopores, is thought to be inextricably linked with the Ohmic nature, extremely stable open-pore current during analyte translocation (hours), minimum analyte sticking with self-correction of current signal (if analyte sticking causes current deviation) and higher analyte responsiveness. The transport phenomena through these chemically modified nanopores are successfully tested by translocating 1 kb dsDNA and the human serum transferrin (hSTf) protein, with the highlight being the yield of an excess of 200 thousand DNA translocation events. Moreover, a comprehensive noise analysis done for the low frequency regime of this new class of SSNs revealed interesting characteristics which are distinct from the conventionally fabricated SSNs.

Experimental study of excessively-long translocation time of single DNA through sub-5 nanometer solid-state nanopores

Excessively-long translocation events of single DNAs are experimentally observed using a small nanopore. Solid-state Nano pores on SiNx membranes with pore diameters less than 5nm are fabricated via Transmission Electron Microscopy. The translocation testing system is set up based on patch-clamp and Lab-on-Chip, and translocation experiments of Lambda DNAs are conducted. Stable current traces and single molecular translocation events are achieved. Statistical analysis under various cross-membrane voltages shows typical characteristics of SiNx Nano pores, including event rates, threshold voltages, and noise power-spectrum-density. Particularly, excessively-long dwell time (>100ms) events through <5 nm nanopore are observed and attributed to the interaction between DNAs and pore walls. This characteristic is compared against the basic current-blockage model as well as that of a 10 nm nanopore control experiment, demonstrating additional blockage effects.

A solid-state nanopore-based single-molecule approach for label-free characterization of plant polysaccharides

Polysaccharides are important biomacromolecules existing in all plants, most of which are integrated into a fibrillar structure called the cell wall. In the absence of an effective methodology for polysaccharide analysis that arises from compositional heterogeneity and structural flexibility, our knowledge of cell wall architecture and function is greatly constrained. Here, we develop a single-molecule approach for identifying plant polysaccharides with acetylated modification levels. We designed a solid-state nanopore sensor supported by a free-standing SiNx membrane in fluidic cells. This device was able to detect cell wall polysaccharide xylans at concentrations as low as 5 ng/μL and discriminate xylans with hyperacetylated and unacetylated modifications. We further demonstrated the capability of this method in distinguishing arabinoxylan and glucuronoxylan in monocot and dicot plants. Combining the data for categorizing polysaccharide mixtures, our study establishes a single-molecule platform for polysaccharide analysis, opening a new avenue for understanding cell wall structures, and expanding polysaccharide applications.

Nanopore Fabrication via Transient High Electric Field Controlled Breakdown and Detection of Single RNA Molecules.

The fabrication of nanopores through a dielectric breakdown method, achieved by simple, low-cost desktop setups, has promoted the research of solid-state nanopore sensing. This paper reports a method for fabricating nanopores. This method uses transient high electric field controlled breakdown (THCBD) to form electric-field-dependent nanopores with different diameters in the order of milliseconds. By manipulating a micropipette with a high electric field to establish the meniscus contact with the SiNx membrane, nanopores can be formed through an "auto-brake" fabrication process. Compared with the traditional dielectric breakdown, THCBD can greatly shorten the breakdown time and form pores of different sizes under higher electric fields without causing additional damage to the SiNx membrane. The nanopores formed by this method can be successfully used to detect two types of RNA molecules. One is transfer RNA from yeast extract and the other is a synthetic RNA oligonucleotide fragment (rArArArArArArArArArArArA).

61‐2: 2‐inch, 2,000‐ppi Silicon Nitride Mask for Patterning Ultra‐High‐Resolution OLED Displays

We developed a 2‐inch, 2000 ppi shadow mask based on micronthin, free‐standing silicon nitride (SiNx) membrane for patterning OLED displays. Its layer composition and fabrication process were optimized to yield an ultra‐flat, self‐tensioned silicon nitride mask (SNM) that can achieve a submicron shadow distance limited only by the thickness of the membrane in line‐of‐sight vacuum depositions.

Confocal scanning photoluminescence for mapping electron and photon beam-induced microscopic changes in SiNx during nanopore fabrication

Focused electron and laser beams have shown the ability to form nanoscale pores in SiNx membranes. During the fabrication process, areas beyond the final nanopore location will inevitably be exposed to the electron beams or the laser beams due to the need for localization, alignment and focus. It remains unclear how these unintended exposures affect the integrity of the membrane. In this work, we demonstrate the use of confocal scanning photoluminescence (PL) for mapping the microscopic changes in SiNx nanopores when exposed to electron and laser beams. We developed and validated a model for the quantitative interpretation of the scanned PL result. The model shows that the scanning PL result is insensitive to the nanopore size. Instead, it is dominated by the product of two microscopic material factors: quantum yield profile (i.e. variations in electronic structure) and thickness profile (i.e. thinning of the membrane). We experimentally demonstrated that the electron and laser beams could alter the material electronic structures (i.e. quantum yield) even when no thinning of the membrane occurs. Our results suggest that minimizing the unintended e-beam or laser beam to the SiNx during the fabrication is crucial if one desires the microscopic integrity of the membrane.

Enhanced Reduction of Thermal Conductivity in Amorphous Silicon Nitride-Containing Phononic Crystals Fabricated Using Directed Self-Assembly of Block Copolymers.

Studies have demonstrated that the thermal conductivity (κ) of crystalline semiconductor materials can be reduced by phonon scattering in periodic nanostructures formed using templates fabricated from self-assembled block copolymers (BCPs). Compared to crystalline materials, the heat transport mechanisms in amorphous inorganic materials differ significantly and have been explored far less extensively. However, thermal management of amorphous inorganic solids is crucial for a broad range of semiconductor devices. Here we present the fabrication of freestanding amorphous silicon nitride (SiNx) membranes for studying κ in an amorphous solid. To form a periodic nanostructure, directed self-assembly of cylinder-forming BCPs is used to pattern in the SiNx highly ordered, hexagonally close packed nanopores with pitch and neck width down to 37.5 and 12 nm, respectively. The κ of the nanoporous SiNx membranes is 60% smaller than the classically predicted value based on just the membrane porosity. In comparison, holes with much larger neck widths and pitches patterned by e-beam lithography lead to only a slight reduction in κ, which is closer to the classical porosity-based prediction. These results demonstrate that κ of amorphous SiNx can be reduced by introducing periodic nanostructures that behave as a phononic crystal, where the relationship between the smallest dimension of the nanostructure and the length scale of the mean-free paths of the dominant, heat-carrying phonons is critical. Additionally, changing the orientation of the hexagonal array of nanopores relative to the primary direction of heat flow has a smaller impact on amorphous SiNx than was previously observed in silicon.

Overview of microfabricated bolometers with vertically aligned carbon nanotube absorbers

Multi-wall vertically aligned carbon nanotubes (VACNTs) are nearly ideal absorbers due to their exceptionally low reflectance over a broad wavelength range. Integrating VACNTs as bolometer absorbers, however, can be difficult due to their high growth temperature and fragile nature. Despite these challenges, we have microfabricated many different types of VACNT bolometers, ranging from cryogenic optical power primary standards to room temperature satellite-based solar irradiance monitors and broadband infrared microbolometers. Advantages our VACNT bolometers provide over the bolometers they replace vary by application, but can be reduced size and time constant, increased absorption, and/or microfabrication instead of hand assembly. Depending on the application and operating conditions, our VACNT bolometers are designed with a variety of thermistors and weak thermal links. The thermistors used include commercial surface mount chips, superconducting transition-edge sensors, and vanadium oxide (VOx). Weak thermal links include silicon nitride (SiNx) membranes, Si bridges, and laser-cut polyimide. We summarize a wide variety of microfabricated bolometers with VACNT absorbers that measure optical power levels spanning over seven orders of magnitude.

Lifetime and Stability of Silicon Nitride Nanopores and Nanopore Arrays for Ionic Measurements.

Nanopores are promising for many applications including DNA sequencing and molecular filtration. Solid-state nanopores are preferable over their biological counterparts for applications requiring durability and operation under a wider range of external parameters, yet few studies have focused on optimizing their robustness. We report the lifetime and durability of pores and porous arrays in 10 to 100 nm-thick, low-stress silicon nitride (SiNx) membranes. Pores are fabricated using a transmission electron microscope (TEM) and/or electron beam lithography (EBL) and reactive ion etching (RIE), with diameters from 2 to 80 nm. We store them in various electrolyte solutions (KCl, LiCl, MgCl2) and record open pore conductance over months to quantify pore stability. Pore diameters increase with time, and diameter etch rate increases with electrolyte concentration from Δd/Δt ∼ 0.2 to ∼ 3 nm/day for 0.01 to 3 M KCl, respectively. TEM confirms the range of diameter etch rates from ionic measurements. Using electron energy loss spectroscopy (EELS), we observe a N-deficient region around the edges of TEM-drilled pores. Pore expansion is caused by etching of the Si/SiO2 pore walls, which resembles the dissolution of silicon found in minerals such as silica (SiO2) in salty ocean water. The etching process occurs where the membrane was exposed to the electron beam and can result in pore formation. However, coating pores with a conformal 1 nm-thick hafnium oxide layer prevents expansion in 1 M KCl, in stark contrast to bare SiNx pores (∼1.7 nm/day). EELS data reveal the atomic composition of bare and HfO2-coated pores.

Surface modification of solid-state nanopore by plasma-polymerized chemical vapor deposition of poly(ethylene glycol) for stable device operation

Biopolymer adsorption onto a membrane is a significant issue in the reliability of solid-state nanopore devices, since it degrades the device performance or promotes device failure. In this work, a poly(ethylene glycol) (PEG) layer was coated on a silicon nitride (SiNx) membrane by plasma-polymerized vapor deposition to inhibit biopolymer adsorption. From optical observations, the deposited PEG layer demonstrated increased hydrophilicity and anti-adsorption property compared to the SiNx surface. Electrical properties of the PEG/SiNx nanopore were characterized, showing Ohmic behavior and a 6.3 times higher flicker noise power due to the flexible conformation of PEG in water. Antifouling performance of each surface was analyzed by measuring the average time from voltage bias to the first adsorption during DNA translocation experiments, where the modified surface enabled two times prolonged device operation. The time to adsorption was dependent on the applied voltage, implying adsorption probability was dominated by the electrophoretic DNA approach to the nanopore. DNA translocation behaviors on each surface were identified from translocation signals, as the PEG layer promoted unfolded and fast movement of DNA through the nanopore. This work successfully analyzed the effect of the PEG layer on DNA adsorption and translocation in solid-state nanopore experiments.

Development of Transition-Edge Sensor X-ray Microcalorimeter Linear Array for Compton Scattering and Energy Dispersive Diffraction Imaging

We present a strip transition-edge sensor microcalorimeter linear array detector developed for energy dispersive X-ray diffraction imaging and Compton scattering applications. The prototype detector is an array of 20 transition-edge-sensors with absorbers in strip geometry arranged in a linear array. We discuss the fabrication steps needed to develop this array including Mo/Cu bilayer, Au electroplating, and proof-of-principle fabrication of long strips of SiNx membranes. We demonstrate minimal unwanted effect of strip geometry on X-ray pulse response, and show linear relationship of 1/pulse height and pulse decay times with absorber length. For the absorber lengths studied, preliminary measurements show energy resolutions of 40 eV to 180 eV near 17 keV. Furthermore, we show that the heat flow to the cold bath is nearly independent of the absorber area and depends on the SiNx membrane geometry.

Biomimetic Signal Propagation in a Two-Pore Solid-State System

A key characteristic of excitable ion channels is the ability to interact with neighboring pores so that localized environmental stimuli can initiate complex large-scale responses, such as an action potential propagating along a neuron. In the case of a nerve signal, this is accomplished through local changes in the membrane voltage and ion concentration inducing nearby pores to change conductance states. The replication of this behavior in synthetic nanopore platforms has the potential to enable new responsive materials useful for biomimetic componentry, drug delivery and filtration technologies. While gating has been demonstrated in synthetic nanopores, previous fabrication methods make it difficult to incorporate such pores into more complex systems due to lack of control over key attributes such as pore location. Here, we fabricate two neighboring nanochannels with controlled spacing such that the transport through one pore can induce a change in conductance of a neighboring pore which has been chemically modified to be ion concentration responsive. The two-pore system is made using focused ion beam nanomachining followed by ion-beam-controlled deposition of SiOx around one pore entrance. Chemistry selective for SiOx is then used to graft single stranded DNA only to the regions where the local deposition was performed providing a final platform that enables local control over the location, size, shape and surface chemistry of each pore in the system. The pore-pore interaction is measured through a step-like increase of the total current passing through the SiNx membrane vs time following a change in applied voltage. We explore the effects of voltage and bulk ionic concentration on the way the inter-pore signal behaves. This successful demonstration of a signal passed from one man-made pore to another is an important step towards the integration of nanopore technology into more complex multi-component systems.

Immobilization of Bioengineered Portal Protein Within a Solid-State Nanopore for Molecular Sensing

Site-specific, reproducible, and uniform-orientation protein immobilization on an inorganic surface while preserving protein conformation and activity is of wide interest for applications in biosensing, protein microarrays, and enzymology, among others. Successful immobilization requires understanding of material's surface chemistry, protein properties, and nature of their interaction to eliminate non-specific binding. Portal protein is a naturally occurring pore (biological nanopore) and part of the bacteriophage packaging machine that pumps the viral genome inside its capsid. In this work, we have explored different approaches to immobilize G20c portal protein from double-stranded bacteriophage G20c into a thin (∼30 nm) silicon nitride (SiNx) membrane embedded in a silicon chip. Desired orientation of the immobilized protein is achieved by maintaining a voltage bias across the membrane to electrokinetically drive a single protein into the synthetic nanopore. The nanopore geometry dictates a predominant favorable protein orientation while the portal preserves its conformation, as indicated by ion current measurements through the “hybrid nanopore”. Application of nanopores (both synthetic and biological) as label-free, single-molecule biosensors for electrical and/or optical probing of structural features in biomolecules have been widely explored. Confirmed by our single-molecule electrical sensing results, our hybrid nanopore system provides mechanically robust and chemically compatible synthetic protein framework, superior to its natural counterparts such as organic membranes (lipid bilayer, for example), and exploits tunable and engineerable characteristics of thermostable G20c portal protein rendering an active, high-resolution biomolecule sensing platform. We demonstrate here through chemical functionalization of synthetic nanopores and/or engineering G20c portal protein assemblies, a protein nanopore chemically linked to a synthetic nanopore, rendering considerably improved protein stability, sensing lifetime, and signal-to-noise ratio compared to our previous hybrid system. This development will be widely applicable to coupled nanopore sensor arrangements such as electro-optical and electro-pressure systems.