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.

Nanopore Fabrication Made Easy: A Portable, Affordable Microcontroller-Assisted Approach for Tailored Pore Formation via Controlled Breakdown.

With growing interest in solid-state nanopore sensing─a single-molecule technique capable of profiling a host of analyte classes─establishing facile and scalable approaches for fabricating molecular-size pores is becoming increasingly important. The introduction of nanopore fabrication by controlled breakdown (CBD) has transformed the economics and accessibility of nanopore fabrication. Here, we introduce the design of an Arduino-based, portable USB-powered CBD device, with an estimated cost of <150 USD, which is ≈10-100× cheaper than most commercial solutions, capable of fabricating single nanopores conducive for single molecule sensing experiments. We demonstrate the facile fabrication of 60 tailored nanopores (∼2.6-12.6 nm) with ∼80% of the pores within 1 nm of the target diameter. Selected pores were then tested with double-stranded DNA, the canonical molecular ruler, demonstrating their performance for single-molecule sensing applications. The device is constructed with off-the-shelf readily available components and controlled using a highly customizable MATLAB application, which has capabilities encompassing pore fabrication, pore enlargement, and current-voltage acquisition for pore size estimation. When combined with a portable amplifier, this device also provides a fully portable sensing platform, an important step toward portable solid-state nanopore sensing applications.

High Accuracy Protein Identification: Fusion of Solid-State Nanopore Sensing and Machine Learning.

Proteins are arguably one of the most important class of biomarkers for health diagnostic purposes. Label-free solid-state nanopore sensing is a versatile technique for sensing and analyzing biomolecules such as proteins at single-molecule level. While molecular-level information on size, shape, and charge of proteins can be assessed by nanopores, the identification of proteins with comparable sizes remains a challenge. Here, solid-state nanopore sensing is combined with machine learning to address this challenge. The translocations of four similarly sized proteins is assessed using amplifiers with bandwidths (BWs) of 100 kHz and 10 MHz, the highest bandwidth reported for protein sensing, using nanopores fabricated in <10 nm thick silicon nitride membranes. F-values of up to 65.9% and 83.2% (without clustering of the protein signals) are achieved with 100 kHz and 10 MHz BW measurements, respectively, for identification of the four proteins. The accuracy of protein identification is further enhanced by classifying the signals into different clusters based on signal attributes, with F-value and specificity of up to 88.7% and 96.4%, respectively, for combinations of four proteins. The combined use of high bandwidth instruments, advanced clustering and machine learning methods allows label-free identification of proteins with high accuracy.

Insights into nanoparticle shape transformation by energetic ions.

Shape modification of embedded nanoparticles can be achieved by means of swift heavy ion irradiation. During irradiation, the particles elongate and align with the direction of the ion beam, presumably due to nanometer-scale phase transitions induced by individual ion impacts. However, the details of this transformation are not fully understood. The shape of metal nanoparticles embedded in dielectric matrices defines the non-linear optical properties of the composite material. Therefore, understanding the transformation process better is beneficial for producing materials with the desired optical properties. We study the elongation mechanism of gold nanoparticles using atomistic simulations. Here we focus on long-timescale processes and adhesion between the nanoparticle and the matrix. Without the necessity of ad-hoc assumptions used earlier, our simulations show that, due to adhesion with the oxide, the nanoparticles can grow in aspect ratio while in the molten state even after silicon dioxide solidifies. Moreover, they demonstrate the active role of the matrix: Only explicit simulations of ion impacts around the embedded nanoparticle provide the mechanism for continuous elongation up to experimental values of aspect ratio. Experimental transmission electron microscopy micrographs of nanoparticles after high-fluence irradiation support the simulations. The elongated nanoparticles in experiments and their interface structures with silica, as characterized by the micrographs, are consistent with the simulations. These findings bring ion beam technology forward as a precise tool for shaping embedded nanostructures for various optical applications.

Understanding the Role of (W, Mo, Sb) Dopants in the Catalyst Evolution and Activity Enhancement of Co3 O4 during Water Electrolysis via In Situ Spectroelectrochemical Techniques.

Unlocking the potential of the hydrogen economy is dependent on achieving green hydrogen (H2 ) production at competitive costs. Engineering highly active and durable catalysts for both oxygen and hydrogen evolution reactions (OER and HER) from earth-abundant elements is key to decreasing costs of electrolysis, a carbon-free route for H2 production. Here, a scalable strategy to prepare doped cobalt oxide (Co3 O4 ) electrocatalysts with ultralow loading, disclosing the role of tungsten (W), molybdenum (Mo), and antimony (Sb) dopants in enhancing OER/HER activity in alkaline conditions, is reported. In situ Raman and X-ray absorption spectroscopies, and electrochemical measurements demonstrate that the dopants do not alter the reaction mechanisms but increase the bulk conductivity and density of redox active sites. As a result, the W-doped Co3 O4 electrode requires ≈390 and ≈560 mV overpotentials to reach ±10 and ±100 mA cm-2 for OER and HER, respectively, over long-term electrolysis. Furthermore, optimal Mo-doping leads to the highest OER and HER activities of 8524 and 634 A g-1 at overpotentials of 0.67 and 0.45 V, respectively. These novel insights provide directions for the effective engineering of Co3 O4 as a low-cost material for green hydrogen electrocatalysis at large scales.

Ultrathin, High-Lifetime Silicon Nitride Membranes for Nanopore Sensing.

Thin membranes are highly sought-after for nanopore-based single-molecule sensing, and fabrication of such membranes becomes challenging in the ≲10 nm thickness regime where a plethora of useful molecule information can be acquired by nanopore sensing. In this work, we present a scalable and controllable method to fabricate silicon nitride (SixNy) membranes with effective thickness down to ∼1.5 nm using standard silicon processing and chemical etching using hydrofluoric acid (HF). Nanopores were fabricated using the controlled breakdown method with estimated pore diameters down to ∼1.8 nm yielding events >500,000 and >1,800,000 from dsDNA and bovine serum albumin (BSA) protein, respectively, demonstrating the high-performance and extended lifetime of the pores fabricated through our membranes. We used two different compositions of SixNy for membrane fabrication (near-stoichiometric and silicon-rich SixNy) and compared them against commercial membranes. The final thicknesses of the membranes were measured using ellipsometry and were in good agreement with the values calculated from the bulk etch rates and DNA translocation characteristics. The stoichiometry and the density of the membrane layers were characterized with Rutherford backscattering spectrometry while the nanopores were characterized using pH-conductance, conductivity-conductance, and power spectral density (PSD) graphs.

SAXS data modelling for the characterisation of ion tracks in polymers.

Here, we present new models to fit small angle X-ray scattering (SAXS) data for the characterization of ion tracks in polymers. Ion tracks in polyethylene terephthalate (PET), polycarbonate (PC), polyimide (PI) and polymethyl methacrylate (PMMA) were created by swift heavy ion irradiation using 197Au and 238U with energies between 185 MeV and 2.0 GeV. Transmission SAXS measurements were performed at the Australian Synchrotron. SAXS data were analysed using two new models that describe the tracks by a cylindrical structure composed of a highly damaged core with a gradual transition to the undamaged material. First, we investigate the 'Soft Cylinder Model', which assumes a smooth function to describe the transition region by a gradual change in density from a core to a matrix. As a simplified and computational less expensive version of the 'Soft Cylinder Model', the 'Core Transition Model' was developed to enable fast fitting. This model assumes a linear increase in density from the core to the matrix. Both models yield superior fits to the experimental SAXS data compared with the often-used simple 'Hard Cylinder Model' assuming a constant density with an abrupt transition.

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

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

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.

Photonic Fractal Metamaterials: A Metal-Semiconductor Platform with Enhanced Volatile-Compound Sensing Performance.

Advance of photonics media is restrained by the lack of structuring techniques for the 3D fabrication of active materials with long-range periodicity. A methodology is reported for the engineering of tunable resonant photonic media with thickness exceeding the plasmonic near-field enhancement region by more than two orders of magnitude. The media architecture consists of a stochastically ordered distribution of plasmonic nanocrystals in a fractal scaffold of high-index semiconductors. This plasmonic-semiconductor fractal media supports the propagation of surface plasmons with drastically enhanced intensity over multiple length scales, overcoming the 2D limitations of established metasurface technologies. The fractal media are used for the fabrication of plasmonic optical gas sensors, achieving a limit of detection of 0.01 vol% at room temperature and sensitivity up to 1.9 nm vol%-1 , demonstrating almost a fivefold increase with respect to an optimized planar geometry. Beneficially to their implementation, the self-assembly mechanism of this fractal architecture allows fabrication of micrometer-thick media over surfaces of several square centimeters in a few seconds. The designable optical features and intrinsic scalability of these photonic fractal metamaterials provide ample opportunities for applications, bridging across transformation optics, sensing, and light harvesting.

Annealing of ion tracks in apatite under pressure characterized in situ by small angle x-ray scattering.

Fission track thermochronology is routinely used to investigate the thermal history of sedimentary basins, as well as tectonic uplift and denudation rates. While the effect of temperature on fission track annealing has been studied extensively to calibrate the application of the technique, the effect of pressure during annealing is generally considered to be negligible. However, a previous study suggested elevated pressure results in a significantly different annealing behaviour that was previously unknown. Here, we present a method to study track annealing in situ under high pressure by using synchrotron-based small angle x-ray scattering (SAXS). To simulate fission tracks in a controlled environment, ion tracks were created in apatite from Durango, Mexico using 2 GeV Au or Bi ions provided by an ion accelerator facility. Samples were annealed at 250 °C at approximately 1 GPa pressure using diamond anvil cells (DACs) with heating capabilities. Additional in situ annealing experiments at ambient pressure and temperatures between 320 and 390 °C were performed for comparison. At elevated pressure a significantly accelerated annealing rate of the tracks was observed compared with annealing at ambient pressure. However, when extrapolated to geologically relevant temperatures and pressures, the effects become very small. The measurement methodology presented provides a new avenue to study materials behaviour in extreme environments.

Ultrafast ion sieving using nanoporous polymeric membranes.

The great potential of nanoporous membranes for water filtration and chemical separation has been challenged by the trade-off between selectivity and permeability. Here we report on nanoporous polymer membranes with an excellent balance between selectivity and permeability of ions. Our membranes are fabricated by irradiating 2-µm-thick polyethylene terephthalate Lumirror® films with GeV heavy ions followed by ultraviolet exposure. These membranes show a high transport rate of K+ ions of up to 14 mol h-1 m-2 and a selectivity of alkali metal ions over heavy metal ions of >500. Combining transport experiments and molecular dynamics simulations with a polymeric nanopore model, we demonstrate that the high permeability is attributable to the presence of nanopores with a radius of ~0.5 nm and a density of up to 5 × 1010 cm-2, and the selectivity is ascribed to the interaction between the partially dehydrated ions and the negatively charged nanopore wall.

Saturation of the ion-hammering effect for large non-hydrostatic capillarity stresses in colloidal silica nanoparticles.

We investigate the role of capillarity stresses on the ion-hammering phenomenon when sub-micrometer colloidal particles are considered. To this end, nearly monodisperse, chemically synthesized silica (SiO2) colloids (100, 300 and 600 nm) were irradiated at room temperature (300 K) with 4 MeV Au ions for fluences up to Φ = 1.8 × 10¹6 cm⁻². It has been taken for granted that the transverse dimension of an ion-deformable amorphous material grows exponentially with the irradiation fluence, L(φ) = L0exp[A0Φ]. Here, we show that for sub-micrometer particles the irradiation-induced deformation saturates for larger fluences, L(φ)→const. The saturation fluence depends on the initial dimension of the colloidal nanoparticles: the smaller the dimension of the colloids, the lower the saturation fluence. Experimental data are successfully accounted for by having recourse to a phenomenological model first developed by Klaumünzer and further elaborated by van Dillen. We also estimate the evolution with fluence of the principal stresses inside the particles, σ11(φ) = σ22(φ) and σ33(φ), and we show that they evolve toward a steady-state value following a sigmoidal-like behavior. Furthermore, when stresses induced by the surface curvature become non-negligible the approximation often made that the deformation strain rate, A0 = dL/L dΦ, remains constant upon irradiation is no longer valid. We show that A0 evolves with the irradiation fluence, e.g. A0→A(Φ), and we relate this behavior to the evolution of the stresses upon irradiation. Finally, this work allows us to define the limits of the ion-hammering effect when the non-hydrostatic capillarity stresses become important.