High Accuracy Protein Identification: Fusion of Solid-State Nanopore Sensing and Machine Learning
Shankar Dutt, Hancheng Shao, Buddini Karawdeniya, Y. M. Nuwan D. Y. Bandara,Elena Daskalaki, Hanna Suominen, and Patrick Kluth
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.
Ion track formation and porosity in InSb induced by swift heavy ion irradiation
Journal of Vacuum Science and Technology A
Taleb Alwadi, Christian Notthoff, Shankar Dutt, Jessica Wierbik, Nahid Afrin, Alexander Kiy, and Patrick Kluth
Ion track formation, irradiation-induced damage (amorphization), and the formation of porosity in InSb after 185 MeV 197Au swift heavy ion irradiation are studied as a function of ion fluence and irradiation angle. Rutherford backscattering spectrometry in channeling geometry reveals an ion track radius of about 16 nm for irradiation normal to the surface and 21 nm for off-normal irradiation at 30° and 60°. Cross-sectional scanning electron microscopy shows significant porosity that increases when irradiation was performed off-normal to the surface. Off-normal irradiation shows a preferential orientation of the pores at about 45° relative to the surface normal. Moreover, when subjected to identical conditions, InSb samples demonstrate notably higher swelling compared to GaSb bulk samples.
Annealing of swift heavy ion tracks in amorphous silicon dioxide
Applied Surface Science
Shankar Dutt, Christian Notthoff, Xue Wang, Christina Trautmann, Pablo Mota-Santiago, Patrick Kluth
The annealing kinetics of the high energy ion damage in amorphous silicon dioxide (a-SiO2) are still not well understood, despite the material's widespread application in material science, physics, geology, and biology. This study investigates how annealing temperature, duration, and ambient environment affect the recovery of irradiation damage produced along the trajectory of swift heavy ions in a-SiO2. The track-annealing kinetics and the changing ion track morphology were investigated using synchrotron-based small-angle X-ray scattering (SAXS) and etching methods. We found that track annealing proceeds quicker near the sample surface demonstrated by a changing track etch rate as a function of depth. Measurements of ion tracks using SAXS show only small changes in the radial density distribution profile of the ion tracks. Activation energy of the annealing process at different sample depths was determined and the effect of the capping layer during the annealing process was also studied. Combination of oxygen diffusion and stress relaxation may contribute to the observed behaviour of preferential and anisotropic healing of the ion track. The results add to the fundamental understanding of ion track damage recovery and may have direct implications for materials for radioactive waste storage and solid state nanopores.
Role of antioxidants in swift heavy ion tracks in polypropylene
Shankar Dutt, Pavel Apel, Olga Polezhaeva, Alexander Kiy, Nahid Afrin, Christian Notthoff, Nigel Kirby, Patrick Kluth
Using synchrotron-based small angle X-ray scattering, ion tracks created in polypropylene foils with different antioxidant contents were investigated. Tracks were created by irradiation with 197Au, 209Bi, and 132Xe ions of energies 2.2 GeV, 710 MeV, and 160 MeV, respectively. The influence of antioxidant concentration in the polymer foils and aging of the samples on the structure of the ion tracks was explored. Polypropylene foils with high antioxidant content show a cylindrical track structure with a highly damaged core with significant mass loss and a gradual transition to the undamaged material. The size of the ion track can directly be correlated to the energy loss. On the other hand, ion tracks in low antioxidant content polypropylene foils exposed to Au/Bi ions reveal a cylindrical core shell structure with an over-dense shell area and a core region that is less dense than the pristine polymer. Oxygen uptake in the foils by the free radicals produced in the shell during the ion irradiation process was attributed to this structure due to prolonged exposure to ambient atmosphere. An overall mass increase was observed for these samples, consistent with the SAXS measurements and additional oxidation in a damaged halo produced by tracks.
Highly Rectifying Conical Nanopores in Amorphous SiO2 Membranes for Nanofluidic Osmotic Power Generation and Electroosmotic Pumps
ACS Applied Nano Materials
Alexander Kiy, Shankar Dutt, Christian Notthoff, Maria E. Toimil-Molares, Nigel Kirby, and Patrick Kluth
Nanopore membranes are a versatile platform for a wide range of applications ranging from medical sensing to filtration and clean energy generation. To attain high-flux rectifying ionic flow, it is required to produce short channels exhibiting asymmetric surface charge distributions. This work reports on a system of track etched conical nanopores in amorphous SiO2 membranes, fabricated using the scalable track etch technique. Pores are fabricated by irradiation of 920 ± 5 nm thick SiO2 windows with 2.2 GeV 197Au ions and subsequent chemical etching. Structural characterization is performed using atomic force microscopy, scanning electron microscopy, small-angle X-ray scattering, ellipsometry, and surface profiling. Conductometric characterization of the pore surface is performed using a membrane containing 16 pores, including an in-depth analysis of ionic transport characteristics. The pores have a tip radius of 5.7 ± 0.1 nm, a half-cone angle of 12.6 ± 0.1°, and a length of 710 ± 5 nm. The pKa, pKb, and pI are determined to 7.6 ± 0.1, 1.5 ± 0.2, and 4.5 ± 0.1, respectively, enabling the fine-tuning of the surface charge density between +100 and −300 mC m–2 and allowing to achieve an ionic current rectification ratio of up to 10. This highly versatile technology addresses some of the challenges that contemporary nanopore systems face and offers a platform to improve the performance of existing applications, including nanofluidic osmotic power generation and electroosmotic pumps.
Ultrathin, High-Lifetime Silicon Nitride Membranes for Nanopore Sensing
Shankar Dutt, Buddini I Karawdeniya, YM Nuwan DY Bandara, Nahid Afrin, Patrick Kluth
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
Physical Chemistry Chemical Physics
Xue Wang, Shankar Dutt, Christian Notthoff, Alexander Kiy, Pablo Mota-Santiago, Stephen T. Mudie, Maria E. Toimil-Molares, Feng Liu, Yugang Wang and Patrick Kluth
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.
Shape of nanopores in track-etched polycarbonate membranes
Journal of Membrane Science
Shankar Dutt, Pavel Apel, Nikolay Lizunov, Christian Notthoff, Qi Wen, Christina Trautmann, Pablo Mota-Santiago, Nigel Kirby, Patrick Kluth
High aspect-ratio nanopores of nearly cylindrical geometry were fabricated by irradiation of 20 μm thick polycarbonate (PC) foils with Pb ions followed by UV sensitization and etching in 5 M NaOH at 60 °C. Synchrotron-based small-angle X-ray scattering (SAXS) was used to study the morphology and size variation of the nanopores as a function of the etching time and ion fluence. The shape of the nanopores was found to be consistent with cylindrical pores with ends tapering off towards the two polymer surfaces in the last ~1.6 μm. The tapered structure of the nanopores in track-etched PC membranes was first observed more than 40 years ago followed by many other studies suggesting that the shape of nanopores in PC membranes deviates from a perfect cylinder and nanopores narrow towards both membrane surfaces. It was also reported that the transport properties of the nanopore membranes are influenced by the tapered structure. However, quantification of the shape of nanopores has remained elusive due to inherent difficulties in imaging the pores using microscopy techniques. The present manuscript reports on the quantitative measurement of the tapered structure of nanopores using SAXS. Determination of this structure was enabled by obtaining high quality SAXS data and the development of appropriate fitting models. The etch rates for both the radius at the polymer surface and the radius of the pore in bulk were calculated. Both etch rates decrease slightly with increasing fluence. This behavior is ascribed to the overlap of track halos which are characterized by cross-linking of the polymer chains. The halo radius was estimated to be approximately 120 nm. The influence of the observed nanopore shape on the pore transport properties was estimated and found to have a significant influence on the water flow rates compared to cylindrical pores. The results enable a better understanding of track-etched membranes and facilitate improved pore design for many applications.
Ion track etching of polycarbonate membranes monitored by in situ small angle X-ray scattering
Physical Chemistry Chemical Physics
Alexander Kiy, Christian Notthoff, Shankar Dutt, Mark Grigg, Andrea Hadley, Pablo Mota-Santiago, Nigel Kirby, Christina Trautmann, Maria E. Toimil-Molares and Patrick Kluth
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.
van der Waals coefficients of the multi-layered MoS2 with alkali metals
Shankar Dutt, Sukhjit Singh, Aman Mahajan, Bindiya Arora and B K Sahoo
The van der Waals coefficients and the separation dependent retardation functions of the interactions between the atomically thin films of the multi-layered transition metal molybdenum disulfide (MoS 2) dichalcogenides with the alkali atoms are investigated. First, we determine the frequency-dependent dielectric permittivity and intrinsic carrier density values for different layers of MoS 2 by adopting various fitting models to the recently measured optical data reported by Yu and co-workers (2015 Sci. Rep. 5, 16 996) using spectroscopy ellipsometry. Then, dynamic electric dipole polarizabilities of the alkali atoms are evaluated very accurately by employing the relativistic coupled-cluster theory. We also demonstrate the explicit change in the above coefficients for different number of layers. These studies are highly useful for the optoelectronics, sensing and storage applications using layered MoS 2.
Analysis of nanometer-sized aligned conical pores using small-angle x-ray scattering
Physical Review Materials
Andrea Hadley, Christina Notthoff, Pablo Mota-Santiago, Shankar Dutt, Stephan Mudie, M. A. Carrillo-Solano, M. E. Toimil-Molares, Christina Trautmann, and Patrick Kluth
Small-angle x-ray scattering (SAXS) was used to quantitatively study the morphology of aligned, monodis- perse conical etched ion tracks in thin films of amorphous SiO2 with aspect ratios of around 6 : 1 and in polycarbonate foils with aspect ratios of around 1000 : 1. This paper presents the measurement procedure and methods developed for the analysis of the scattering images and shows results obtained for the two material systems. To enable accurate parameter extraction from the data collected from conical scattering objects, a model fitting the two-dimensional (2D) detector images was developed. The analysis involved fitting images from a sequence of measurements with different sample tilts to minimize errors, which may have been introduced due to the experimental setup. The model was validated by the exploitation of the geometric relationship between the sample tilt angle and the cone opening angle, to an angle observed in the features of the SAXS images. We also demonstrate that a fitting procedure for 1D data extracted from the scattering images using a hard cylinder model can also be used to extract the cone size. The application of these techniques enables us to reconstruct the cone morphologies with unprecedented precision.
Structural and electrical characterization of semiconducting xCuO-(100-x) TeO2 glasses
Journal of Non-Crystalline Solids
Navjot Kaur, Atul Khanna, Margit Fábián, Shankar Dutt
Structural, thermal and electrical properties of semiconducting copper tellurite glasses: xCuO-(100-x)TeO2 (x = 30, 40 and 50 mol%) were studied by neutron diffraction, Raman spectroscopy, thermal analysis and two probe electrical conductivity measurements. Reverse Monte Carlo simulations of the neutron structure factors found that Tesingle bondO and Cusingle bondO bonds have equal lengths of 1.94 Å and that both Te and Cu ions exist in structural units of similar size and geometry. The average Cu-O co-ordination decreases from 3.72 to 3.68, while the Te-O co-ordination decreases from 3.48 to 3.34 on increasing the CuO concentration from 30 to 50 mol%. The electrical conductivity increases from 2.96 × 10−9 Ω−1 m−1 to 1.25 × 10−7 Ω−1 m−1 with an increase in CuO concentration from 30 to 50 mol%. The increase in CuO mol% increases the Cusingle bondCu coordination number from 0.68 to 1.26 and promotes electronic hopping between the adjacent Cu sites
High-charge relativistic electron bunches from a kHz laser-plasma accelerator
Physical Review Accelerators and Beams
D. Gustas, D. Guénot, A. Vernier, S. Dutt, F. Böhle, R. Lopez-Martens, A. Lifschitz, and J. Faure
We report on electron wakefield acceleration in the resonant bubble regime with few-millijoule near-single-cycle laser pulses at a kilohertz repetition rate. Using very tight focusing of the laser pulse in conjunction with microscale supersonic gas jets, we demonstrate a stable relativistic electron source with a high charge per pulse up to 24 pC/shot. The corresponding average current is 24 nA, making this kilohertz electron source useful for various applications.