arXiv subjects

Aleksandra Radenovic

Publications and source records attributed to Aleksandra Radenovic.

At least 37 records · Page 2Linked to original sources

arXiv2021

Direct growth of hexagonal boron nitride on photonic chips for high-throughput characterization

Adapting optical microscopy methods for nanoscale characterization of defects in two-dimensional (2D) materials is a vital step for photonic on-chip devices. To increase the analysis throughput, waveguide-based on-chip imaging platforms have been recently developed. Their inherent disadvantage, however, is the necessity to transfer the 2D material from the growth substrate to the imaging chip which introduces contamination, potentially altering the characterization results. Here we present a unique approach to circumvent these shortfalls by directly growing a widely-used 2D material (hexagonal boron nitride, hBN) on silicon nitride chips, and optically characterizing the defects in the intact as-grown material. We compare the direct growth approach to the standard wet transfer method, and confirm the clear advantages of the direct growth. While demonstrated with hBN in the current work, the method is easily extendable to other 2D materials.

physics.optics↗

arXiv2021

Anomalous interfacial dynamics of single proton charges in binary aqueous solutions

Understanding the dynamics of charge exchange between a solid surface and a liquid is fundamental to various situations, ranging from nanofiltration to catalysis and electrochemistry. Charge transfer is ultimately determined by physicochemical processes (surface group dissociation, ion adsorption, etc...) occurring in the few layers of molecules at the interface between the solid and the liquid. Unfortunately, these processes remain largely uncharted due to the experimental challenges in probing interfacial charge dynamics with sufficiently high spatial and temporal resolution. Here, we resolve at the single-charge scale, the dynamics of proton charges at the interface between an hBN crystal and binary mixtures of water and organic amphiphilic solvents (e.g. alcohol), evidencing a dramatic influence of solvation on interfacial dynamics. Our observations rely on the application of spectral Single Molecule Localization Microscopy (sSMLM) to two types of optically active defects at the hBN surface, which act as intrinsic optical markers for both surface protonation and interaction with apolar alkyl groups of the organic solvent. We use sSMLM to reveal interfacial proton charge transport as a succession of jumps between the titratable surface defects, mediated by the transport of the solvated proton charge along the solid/liquid interface. By changing the relative concentration of water in binary mixtures, we evidence a non-trivial effect on interfacial proton charge dynamics, leading at intermediate water concentration to an increased affinity of the proton charge to the solid surface, accompanied by an increased surface diffusivity. These measurements confirm the strong role of solvation on interfacial proton charge transport and establish the potential of single-molecule localization techniques to probe a wide range of dynamic processes at solid/liquid interfaces.

cond-mat.soft↗

arXiv2020

Quantifying the effect of image compression on supervised learning applications in optical microscopy

The impressive growth of data throughput in optical microscopy has triggered a widespread use of supervised learning (SL) models running on compressed image datasets for efficient automated analysis. However, since lossy image compression risks to produce unpredictable artifacts, quantifying the effect of data compression on SL applications is of pivotal importance to assess their reliability, especially for clinical use. We propose an experimental method to evaluate the tolerability of image compression distortions in 2D and 3D cell segmentation SL tasks: predictions on compressed data are compared to the raw predictive uncertainty, which is numerically estimated from the raw noise statistics measured through sensor calibration. We show that predictions on object- and image-specific segmentation parameters can be altered by up to 15% and more than 10 standard deviations after 16-to-8 bits downsampling or JPEG compression. In contrast, a recently developed lossless compression algorithm provides a prediction spread which is statistically equivalent to that stemming from raw noise, while providing a compression ratio of up to 10:1. By setting a lower bound to the SL predictive uncertainty, our technique can be generalized to validate a variety of data analysis pipelines in SL-assisted fields.

eess.IV↗

arXiv2020

Wetting of nanopores probed with pressure

Nanopores are both a tool to study single-molecule biophysics and nanoscale ion transport, but also a promising material for desalination or osmotic power generation. Understanding the physics underlying ion transport through nano-sized pores allows better design of porous membrane materials. Material surfaces can present hydrophobicity, a property which can make them prone to formation of surface nanobubbles. Nanobubbles can influence the electrical transport properties of such devices. We demonstrate an approach which uses hydraulic pressure to probe the electrical transport properties of solid state nanopores. We show how pressure can be used to wet pores, and how it allows control over bubbles in the nanometer scale range normally unachievable using only an electrical driving force. Molybdenum disulfide is then used as a typical example of a 2D material on which we demonstrate wetting and bubble induced nonlinear and linear conductance in the regimes typically used with these experiments. We show that by using pressure one can identify and evade wetting artifacts.

cond-mat.soft↗

arXiv2020

Recent Advances and Prospects in the Research of Nascent Adhesions

Nascent adhesions are submicron transient structures promoting the early adhesion of cells to the extracellular matrix. Nascent adhesions typically consist of several tens of integrins, and serve as platforms for the recruitment and activation of proteins to build mature focal adhesions. They are also associated with early stage signalling and the mechanoresponse. Despite their crucial role in sampling the local extracellular matrix, very little is known about the mechanism of their formation. Consequently, there is a strong scientific activity focused on elucidating the physical and biochemical foundation of their development and function. Precisely the results of this effort will be summarized in this article.

q-bio.SC↗

arXiv2020

Pressure Induced Enlargement and Ionic Current Rectification in Symmetric Nanopores

Nanopores in solid state membranes are a tool able to probe nanofluidic phenomena or can act as a single molecular sensor. They also have diverse applications in filtration, desalination or osmotic power generation. Many of these applications involve chemical, or hydrostatic pressure differences, which act on both the supporting membrane and the ion transport through the pore. By using pressure differences between the sides of the membrane, and an alternating current approach to probe ion transport, we investigate two distinct physical phenomena: the elastic deformation of the membrane through the measurment of strain at the nanopore, and the growth of ionic current rectification with pressure due to pore entrance effects.

cond-mat.soft↗

arXiv2020

Electrochemical Surface Modification of a 2D MoS2 Semiconductor

The surface modification of 2D semiconducting materials, such as transition metal dichalcogenides (TMDCs), is becoming important for a diverse range of applications, such as biosensing, catalysis, energy generation and energy storage. Due to the chemical inertness of their basal plane, the surface modification of 2D TMDCs is mainly limited to their defective sites, or it requires a conversion of TMDC from its semiconducting into a metallic phase. In this work, we show that the basal plane of a 2D semiconductor molybdenum disulfide (MoS2) can be modified by electrochemical grafting of aryl-diazonium salt, such as 3,5-bis(trifluoromethyl)benzenediazonium tetrafluoroborate. To investigate the applicability of this method, we perform electrografting on MoS2 nanoribbons by addressing them individually via a different electrode. High spatial selectivity of this method on the nanoscale opens the possibility for specific surface modification of neighboring 2D layers and nanostructures that are contacted by electrodes. This method could be potentially applicable to other 2D semiconducting materials that are active in the same potential window in which the electrochemical reduction of aryl diazonium salts occurs.

physics.app-ph↗

arXiv2020

Super-resolved optical mapping of reactive sulfur-vacancy in 2D transition metal dichalcogenides

Transition metal dichalcogenides (TMDs) represent an entire new class of semiconducting 2D materials with exciting properties. Defects in 2D TMDs can crucially affect their physical and chemical properties. However, characterization of the presence and spatial distribution of defects is limited either in throughput or in resolution. Here, we demonstrate large area mapping of reactive sulfur-deficient defects in 2D-TMDs coupling single-molecule localization microscopy with fluorescence labeling using thiol chemistry. Our method, reminiscent of PAINT strategies, relies on the specific binding by reversible physisorption of fluorescent probes to sulfur-vacancies via a thiol group and their intermittent emission to apply localization of the labeled defects with a precision down to 15 nm. Tuning the distance between the fluorophore and the docking thiol site allows us to control Föster Resonance Energy Transfer (FRET) process and reveal large structural defects such as grain boundaries and line defects, due to the local irregular lattice structure. Our methodology provides a simple and fast alternative for large-scale mapping of non-radiative defects in 2D materials and paves the way for in-situ and spatially resolved monitoring of the interaction between chemical agent and the defects in 2D materials that has general implications for defect engineering in aqueous condition.

physics.app-ph↗

arXiv2020

Microscopic Transport Analysis of Single Molecule Detection in MoS$_2$ Nanopore Membranes

A microscopic physical analysis of the various resistive effects involved in the electronic detection of single biomolecules in a nanopore of a MoS2 nanoribbon is presented. The analysis relies on a combined experimental-theoretical approach, where the variations of the transverse electronic current along the two-dimensional (2D) membrane due to the translocation of DNA and proteins molecules through the pore are compared with model calculations based on molecular dynamics (MD) and Boltzmann transport formalism for evaluating the membrane conductance. Our analysis that points to a self-consistent interaction among ions, charge carriers around the pore rim and biomolecules, emphasizes the effects of the electrolyte concentration, pore size, nanoribbon geometry, but also the doping polarity of the nanoribbon on the electrical sensitivity of the nanopore in detecting biomolecules, which agrees well with the experimental data.

cond-mat.mes-hall↗

arXiv2020

Self-blinking Dyes unlock High-order and Multi-plane Super-resolution Optical Fluctuation Imaging

Diffraction unlimited super-resolution imaging critically depends on the switching of fluorophores between at least two states, often induced using intense laser light and special buffers. The high illumination power or UV light required for appropriate blinking kinetics is currently hindering live-cell experiments. Recently, so-called self-blinking dyes that switch spontaneously between an open, fluorescent "on"-state and a closed colorless "off"-state were introduced. Here we exploit the synergy between super-resolution optical fluctuation imaging (SOFI) and spontaneously switching fluorophores for 2D functional and for volumetric imaging. SOFI tolerates high labeling densities, on-time ratios, and low signal-to-noise by analyzing higher-order statistics of a few hundred to thousand frames of stochastically blinking fluorophores. We demonstrate 2D imaging of fixed cells with a uniform resolution up to 50-60 nm in 6th order SOFI and characterize changing experimental conditions. We extend multiplane cross-correlation analysis to 4th order using biplane and 8-plane volumetric imaging achieving up to 29 (virtual) planes. The low laser excitation intensities needed for self-blinking SOFI are ideal for live-cell imaging. We show proof-of-principal time-resolved imaging by observing slow membrane movements in cells. Self-blinking SOFI provides a route for easy-to-use 2D and 3D high-resolution functional imaging that is robust against artefacts and suitable for live-cell imaging.

physics.optics↗

arXiv2019

Direct observation of water mediated single proton transport between hBN surface defects

Aqueous proton transport at interfaces is ubiquitous and crucial for a number of fields, ranging from cellular transport and signaling, to catalysis and membrane science. However, due to their light mass, small size and high chemical reactivity, uncovering single proton surface transport at room temperature and in aqueous environment has so far remained out-of-reach of conventional atomic-scale surface science techniques, such as STM. Here, we use single-molecule localization microscopy techniques to resolve optically the transport of individual excess protons at the interface of hexagonal boron nitride crystals and aqueous solutions at room temperature. Our label-free approach relies on the successive protonation and activation of optically active defects at the surface of the crystal allowing us to resolve interfacial proton transport at the single molecule scale with nanometric resolution and over micrometer range. Proton trajectories are revealed as a succession of jumps between proton-binding defects, mediated by interfacial water. We demonstrate unexpected interfacial proton mobility under illumination, limited by proton desorption from individual defects. The proposed mechanism is supported by ab initio molecular dynamics simulations of defected and pristine hBN/water interface. Our observations provide direct experimental evidence at the single molecule scale that interfacial water provides a preferential pathway for lateral proton transport. Our findings have fundamental and general implications for water-mediated molecular charge transport at interfaces.

cond-mat.mes-hall↗

arXiv2019

Nanocapillary Confinement of Imidazolium Based Ionic Liquids

Room temperature ionic liquids are salts which are molten at or around room temperature without any added solvent or solution. In bulk they exhibit glass like dependence of conductivity with temperature as well as coupling of structural and transport properties. Interfaces of ionic liquids have been found to induce structural changes with evidence of long range structural ordering on solid-liquid interfaces spanning length scales of $10-100$nm. Our aim is to characterize the influence of confinement on the structural properties of ionic liquids. We present first conductivity measurements on ionic liquids of the imidazolium type in single conical glass nanopores with confinements as low as tens of nanometers. We probe glassy dynamics of ionic liquids in a large range of temperatures ($-20$ to $70^\circ$C) and nanopore opening sizes ($20-600$nm) in silica glass nanocapillaries. Our results indicate no long range freezing effects due to confinement in nanopores with diameters as low as $20$nm. The studied ionic liquids are found to behave as glass like liquids across the whole accessible confinement size and temperature range.

physics.app-ph↗

arXiv2019

Spectral Cross-Cumulants for Multicolor Super-resolved SOFI Imaging

Super-resolution optical fluctuation imaging (SOFI) provides a resolution beyond the diffraction limit by analysing stochastic fluorescence fluctuations with higher-order statistics. Using nth order spatio-temporal cross-cumulants the spatial resolution as well as the sampling can be increased up to n-fold in all three spatial dimensions. In this study, we extend the cumulant analysis into the spectral domain and propose a novel multicolor super-resolution scheme. The simultaneous acquisition of two spectral channels followed by spectral cross-cumulant analysis and unmixing increase the spectral sampling. The number of discriminable fluorophore species is thus not limited to the number of physical detection channels. Using two color channels, we demonstrate spectral unmixing of three fluorophore species in simulations and multiple experiments with different cellular structures, fluorophores and filter sets. Based on an eigenvalue/ vector analysis we propose a scheme for an optimized spectral filter choice. Overall, our methodology provides a novel route for easy-to-implement multicolor sub-diffraction imaging using standard microscopes while conserving the spatial super-resolution property. This makes simultaneous multiplexed super-resolution fluorescence imaging widely accessible to the life science community interested to probe colocalization between two or more molecular species.

physics.optics↗

arXiv2019

Wide-field spectral super-resolution mapping of optically active defects in hBN

Point defects can have significant impacts on the mechanical, electronic and optical properties of materials. The development of robust, multidimensional, high-throughput and large-scale characterization techniques of defects is thus crucial, from the establishment of integrated nanophotonic technologies to material growth optimization. Here, we demonstrate the potential of wide-field spectral single-molecule localization microscopy (spectral SMLM) for the determination of ensemble spectral properties, as well as characterization of spatial, spectral and temporal dynamics of single defects in CVD-grown and irradiated exfoliated hexagonal boron-nitride (hBN) materials. We characterize the heterogeneous spectral response of our samples, and identify at least two types of defects in CVD-grown materials, while irradiated exfoliated flakes show predominantly only one type of defect. We analyze the blinking kinetics and spectral emission for each type of defects, and discuss their implications with respect to the observed spectral heterogeneity of our samples. Our study shows the potential of wide-field spectral SMLM techniques in material science and paves the way towards quantitative multidimensional mapping of defect properties.

physics.optics↗

arXiv2019

Light Enhanced Blue Energy Generation using MoS$_2$ Nanopores

Blue energy relies on the chemical potential difference generated between solutions of high and low ionic strength and would provide a sun-and-wind independent energy source at estuaries around the world. Converting this osmotic energy through reverse-electrodialysis relies on ion-selective membranes. A novel generation of these membranes is based on atomically thin MoS$_2$ membranes to decrease the resistance to current flow to increase power output. By modulating the surface charge by light we are able to raise the ion selectivity of the membrane by a factor of 5 while staying at a neutral pH. Furthermore, we find that the behavior of small nanopores is dominated by surface conductance. We introduce a formalism based on the Dukhin number to quantify these effects in the case of a concentration gradient system. As a consequence, the charges created by light illumination provoke two important changes. Increased surface charge at the pore rim enhances the ion selectivity and therefore larger osmotic voltage (dominating in small pores), while the increased surface charge of the overall membrane enhances the surface conductance and therefore the osmotic current (dominating in larger pores). The combination of these effects might be able to efficiently boost the energy generation with arrays of nanopores with varying pore sizes.

physics.app-ph↗

arXiv2017

Imaging of optically active defects with nanometer resolution

Point defects significantly influence the optical and electrical properties of solid-state materials due to their interactions with charge carriers, which reduce the band-to-band optical transition energy. There has been a demand for developing direct optical imaging methods that would allow in-situ characterization of individual defects with nanometer resolution. Here, we demonstrate the localization and quantitative counting of individual optically active defects in monolayer hexagonal boron nitride using single molecule localization microscopy. By exploiting the blinking behavior of defect emitters to temporally isolate multiple emitters within one diffraction limited region, we could resolve two defect emitters with a point-to-point distance down to ten nanometers. The results and conclusion presented in this work add unprecedented dimensions towards future applications of defects in quantum information processing and biological imaging.

cond-mat.mes-hall↗

arXiv2017

Investigating the inner structure of focal adhesions with single-molecule localization microscopy

Cells rely on focal adhesions (FAs) to carry out a variety of important tasks, including motion, environmental sensing, and adhesion to the extracellular matrix. Although attaining a fundamental characterization of FAs is a compelling goal, their extensive complexity and small size, which can be below the diffraction limit, have hindered a full understanding. In this study we have used single-molecule localization microscopy (SMLM) to investigate integrin $β$3 and paxillin in rat embryonic fibroblasts growing on two different extracellular matrix-representing substrates (i.e. fibronectin-coated substrates and specifically bio-functionalized nano-patterned substrates). To quantify the substructure of FAs, we developed a method based on expectation maximization of a Gaussian mixture that accounts for localization uncertainty and background. Analysis of our SMLM data indicates that the structures within FAs, characterized as a Gaussian mixture, typically have areas between 0.01 and 1 $μ$m$^2$, contain 10 to 100 localizations, and can exhibit substantial eccentricity. Our approach based on SMLM opens new avenues for studying structural and functional biology of molecular assemblies that display substantial varieties in size, shape, and density.

physics.bio-ph↗

arXiv2016

Complementarity of PALM and SOFI for super-resolution live cell imaging of focal adhesions

Live cell imaging of focal adhesions requires a sufficiently high temporal resolution, which remains a challenging task for super-resolution microscopy. We have addressed this important issue by combining photo-activated localization microscopy (PALM) with super-resolution optical fluctuation imaging (SOFI). Using simulations and fixed cell focal adhesion images, we investigated the complementarity between PALM and SOFI in terms of spatial and temporal resolution. This PALM-SOFI framework was used to image focal adhesions in living cells, while obtaining a temporal resolution below 10 s. We visualized the dynamics of focal adhesions, and revealed local mean velocities around 190 nm per minute. The complementarity of PALM and SOFI was assessed in detail with a methodology that integrates a quantitative resolution and signal-to-noise metric. This PALM and SOFI concept provides an enlarged quantitative imaging framework, allowing unprecedented functional exploration of focal adhesions through the estimation of molecular parameters such as the fluorophore density and the photo-activation and photo-switching rates.

physics.bio-ph↗