Monitoring Electrochemical Dynamics through Single-Molecule Imaging of hBN Surface Emitters in Organic Solvents

E. Mayner; N. Ronceray; M. Lihter; T-H. Chen; K. Watanabe et al. 

Electrochemical techniques conventionally lack spatial resolution and average local information over an entire electrode. While advancements in spatial resolution have been made through scanning probe methods, monitoring dynamics over large areas is still challenging, and it would be beneficial to be able to decouple the probe from the electrode itself. In this work, we leverage single molecule microscopy to spatiotemporally monitor analyte surface concentrations over a wide area using unmodified hexagonal boron nitride (hBN) in organic solvents. Through a sensing scheme based on redox-active species interactions with fluorescent emitters at the surface of hBN, we observe a region of a linear decrease in the number of emitters against increasingly positive potentials applied to a nearby electrode. We find consistent trends in electrode reaction kinetics vs overpotentials between potentiostat-reported currents and optically read emitter dynamics, showing Tafel slopes greater than 290 mV·decade-1. Finally, we draw on the capabilities of spectral single-molecule localization microscopy (SMLM) to monitor the fluorescent species’ identity, enabling multiplexed readout. Overall, we show dynamic measurements of analyte concentration gradients on a micrometer-length scale with nanometer-scale depth and precision. Considering the many scalable options for engineering fluorescent emitters with two-dimensional (2D) materials, our method holds promise for optically detecting a range of interacting species with exceptional localization precision.

Nanofluidic logic with mechano-ionic memristive switches

T. Emmerich; Y. Teng; N. Ronceray; E. Lopriore; R. Chiesa et al. 

Neuromorphic systems are typically based on nanoscale electronic devices, but nature relies on ions for energy-efficient information processing. Nanofluidic memristive devices could thus potentially be used to construct electrolytic computers that mimic the brain down to its basic principles of operation. Here we report a nanofluidic device that is designed for circuit-scale in-memory processing. The device, which is fabricated using a scalable process, combines single-digit nanometric confinement and large entrance asymmetry and operates on the second timescale with a conductance ratio in the range of 9 to 60. In operando optical microscopy shows that the memory capabilities are due to the reversible formation of liquid blisters that modulate the conductance of the device. We use these mechano-ionic memristive switches to assemble logic circuits composed of two interactive devices and an ohmic resistor.

Open-source microscope add-on for structured illumination microscopy

M. T. M. Hannebelle; E. Raeth; S. M. Leitao; T. Lukes; J. Pospisil et al. 

Super-resolution techniques expand the abilities of researchers who have the knowledge and resources to either build or purchase a system. This excludes the part of the research community without these capabilities. Here we introduce the openSIM add-on to upgrade existing optical microscopes to Structured Illumination super-resolution Microscopes (SIM). The openSIM is an open-hardware system, designed and documented to be easily duplicated by other laboratories, making super-resolution modality accessible to facilitate innovative research. The add-on approach gives a performance improvement for pre-existing lab equipment without the need to build a completely new system.|Researchers developed an open-hardware structured illumination microscopy add-on. This affordable upgrade provides super-resolution capabilities for normal optical microscopes. Detailed instructions enable easy reproduction to help democratize advanced microscopy.

Fluorescence microscopy: A statistics-optics perspective

M. Fazel; K. S. Grussmayer; B. Ferdman; A. Radenovic; Y. Shechtman et al. 

Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Accounting for these features is often critical in quantitatively interpreting microscopy images, especially those gathering information at scales on par with or smaller than light’s emission wavelength. Here the optics responsible for generating fluorescent images, fluorophore properties, and microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement, are reviewed.

Label-Free Techniques for Probing Biomolecular Condensates

K. A. Ibrahim; A. S. Naidu; H. Miljkovic; A. Radenovic; W. Yang 

Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and expansive library of tools has been developed to investigate various aspects and properties, encompassing structural and compositional information, material properties, and their evolution throughout the life cycle from formation to eventual dissolution. This Review presents an overview of the expanded set of tools and methods that researchers use to probe the properties of biomolecular condensates across diverse scales of length, concentration, stiffness, and time. In particular, we review recent years’ exciting development of label-free techniques and methodologies. We broadly organize the set of tools into 3 categories: (1) imaging-based techniques, such as transmitted-light microscopy (TLM) and Brillouin microscopy (BM), (2) force spectroscopy techniques, such as atomic force microscopy (AFM) and the optical tweezer (OT), and (3) microfluidic platforms and emerging technologies. We point out the tools’ key opportunities, challenges, and future perspectives and analyze their correlative potential as well as compatibility with other techniques. Additionally, we review emerging techniques, namely, differential dynamic microscopy (DDM) and interferometric scattering microscopy (iSCAT), that have huge potential for future applications in studying biomolecular condensates. Finally, we highlight how some of these techniques can be translated for diagnostics and therapy purposes. We hope this Review serves as a useful guide for new researchers in this field and aids in advancing the development of new biophysical tools to study biomolecular condensates.

Optical imaging of molecules and their dynamics from surfaces to nanoscale confinement

Tunnel junction sensing of TATP explosive at the single-molecule level

A. Z. Tomovic; H. Miljkovic; M. S. Drazic; V. P. Jovanovic; R. Zikic 

Triacetone triperoxide (TATP) is a highly potent homemade explosive commonly used in terrorist attacks. Its detection poses a significant challenge due to its volatility, and the lack of portability of current sensing techniques. To address this issue, we propose a novel approach based on single-molecule TATP detection in the air using a device where tunneling current in N-terminated carbon-nanotubes nanogaps is measured. By employing the density functional theory combined with the non-equilibrium Green’s function method, we show that current of tens of nanoamperes passes through TATP trapped in the nanogap, with a discrimination ratio of several orders of magnitude even against prevalent indoor volatile organic compounds (VOCs). This high tunneling current through TATP’s highest occupied molecular orbital (HOMO) is facilitated by the strong electric field generated by N-C polar bonds at the electrode ends and by the hybridization between TATP and the electrodes, driven by oxygen atoms within the probed molecule. The application of the same principle is discussed for graphene nanogaps and break-junctions.|This DFT+NEGF study explores the sensing of the TATP explosive at a single molecule level. The real-time sensing via tunneling current measurement of a TATP molecule between N-terminated (3,3) CNT electrodes could be a solution for portable devices.

Confinement-Controlled Water Engenders Unusually High Electrochemical Capacitance

S. Melnik; A. Ryzhov; A. Kiselev; A. Radenovic; T. Weil et al. 

The electrodynamicsof nanoconfined water have been shownto changedramatically compared to bulk water, opening room for safe electrochemicalsystems. We demonstrate a nanofluidic “water-only” batterythat exploits anomalously high electrolytic properties of pure waterat firm confinement. The device consists of a membrane electrode assemblyof carbon-based nanomaterials, forming continuously interconnectedwater-filled nanochannels between the separator and electrodes. Theefficiency of the cell in the 1-100 nm pore size range showsa maximum energy density at 3 nm, challenging the region of the currentmetal-ion batteries. Our results establish the electrodynamic fundamentalsof nanoconfined water and pave the way for low-cost and inherentlysafe energy storage solutions that are much needed in the renewableenergy sector.

Selective Growth of van der Waals Heterostructures Enabled by Electron-Beam Irradiation

J. Sitek; K. Czerniak-Losiewicz; A. P. Gertych; M. Giza; P. Dabrowski et al. 

Van der Waals heterostructures (vdWHSs) enable the fabricationof complex electronic devices based on two-dimensional (2D) materials.Ideally, these vdWHSs should be fabricated in a scalable and repeatableway and only in the specific areas of the substrate to lower the numberof technological operations inducing defects and impurities. Here,we present a method of selective fabrication of vdWHSs via chemicalvapor deposition by electron-beam (EB) irradiation. We distinguishtwo growth modes: positive (2D materials nucleate on the irradiatedregions) on graphene and tungsten disulfide (WS2) substrates,and negative (2D materials do not nucleate on the irradiated regions)on the graphene substrate. The growth mode is controlled by limitingthe air exposure of the irradiated substrate and the time betweenirradiation and growth. We conducted Raman mapping, Kelvin-probe forcemicroscopy, X-ray photoelectron spectroscopy, and density-functionaltheory modeling studies to investigate the selective growth mechanism.We conclude that the selective growth is explained by the competitionof three effects: EB-induced defects, adsorption of carbon species,and electrostatic interaction. The method here is a critical steptoward the industry-scale fabrication of 2D-materials-based devices.

Nature-Inspired Stalactite Nanopores for Biosensing and Energy Harvesting

A. Chernev; Y. Teng; M. Thakur; V. Boureau; L. Navratilova et al. 

Nature provides a wide range of self-assembled structures from the nanoscale to the macroscale. Under the right thermodynamic conditions and with the appropriate material supply, structures like stalactites, icicles, and corals can grow. However, the natural growth process is time-consuming. This work demonstrates a fast, nature-inspired method for growing stalactite nanopores using heterogeneous atomic deposition of hafnium dioxide at the orifice of templated silicon nitride apertures. The stalactite nanostructures combine the benefits of reduced sensing region typically for 2-dimensional material nanopores with the asymmetric geometry of capillaries, resulting in ionic selectivity, stability, and scalability. The proposed growing method provides an adaptable nanopore platform for basic and applied nanofluidic research, including biosensing, energy science, and filtration technologies.

Spatially multiplexed single-molecule translocations through a nanopore at controlled speeds

S. M. Leitao; V. Navikas; H. Miljkovic; B. Drake; S. Marion et al. 

In current nanopore-based label-free single-molecule sensing technologies, stochastic processes influence the selection of translocating molecule, translocation rate and translocation velocity. As a result, single-molecule translocations are challenging to control both spatially and temporally. Here we present a method using a glass nanopore mounted on a three-dimensional nanopositioner to spatially select molecules, deterministically tethered on a glass surface, for controlled translocations. By controlling the distance between the nanopore and glass surface, we can actively select the region of interest on the molecule and scan it a controlled number of times and at a controlled velocity. Decreasing the velocity and averaging thousands of consecutive readings of the same molecule increases the signal-to-noise ratio by two orders of magnitude compared with free translocations. We demonstrate the method’s versatility by assessing DNA-protein complexes, DNA rulers and DNA gaps, achieving down to single-nucleotide gap detection. In single-molecule characterization, the near-infinite re-read capability on the same region of interest has the potential to unlock greater sensing capacity. A nanopore-based method, named scanning ion conductance spectroscopy, provides complete control over the translocation speed and nanopore position along a selected region and can detect a single 3 angstrom gap in a long strand of DNA.

Nanoscale thermal control of a single living cell enabled by diamond heater-thermometer

A. M. Romshin; V. Zeeb; E. Glushkov; A. Radenovic; A. G. Sinogeikin et al. 

We report a new approach to controllable thermal stimulation of a single living cell and its compartments. The technique is based on the use of a single polycrystalline diamond particle containing silicon-vacancy (SiV) color centers. Due to the presence of amorphous carbon at its intercrystalline boundaries, such a particle is an efficient light absorber and becomes a local heat source when illuminated by a laser. Furthermore, the temperature of such a local heater is tracked by the spectral shift of the zero-phonon line of SiV centers. Thus, the diamond particle acts simultaneously as a heater and a thermometer. In the current work, we demonstrate the ability of such a Diamond Heater-Thermometer (DHT) to locally alter the temperature, one of the numerous parameters that play a decisive role for the living organisms at the nanoscale. In particular, we show that the local heating of 11-12 degrees C relative to the ambient temperature (22 degrees C) next to individual HeLa cells and neurons, isolated from the mouse hippocampus, leads to a change in the intracellular distribution of the concentration of free calcium ions. For individual HeLa cells, a long-term (about 30 s) increase in the integral intensity of Fluo-4 NW fluorescence by about three times is observed, which characterizes an increase in the [Ca2+](cyt) concentration of free calcium in the cytoplasm. Heating near mouse hippocampal neurons also caused a calcium surge-an increase in the intensity of Fluo-4 NW fluorescence by 30% and a duration of similar to 0.4 ms.

The Three-Phase Contact Potential Difference Modulates the Water Surface Charge

V. Artemov; L. Frank; R. Doronin; P. Staerk; A. Schlaich et al. 

The surface charge of an open water surface is crucialfor solvationphenomena and interfacial processes in aqueous systems. However, themagnitude of the charge is controversial, and the physical mechanismof charging remains incompletely understood. Here we identify a previouslyoverlooked physical mechanism determining the surface charge of water.Using accurate charge measurements of water microdrops, we demonstratethat the water surface charge originates from the electrostatic effectsin the contact line vicinity of three phases, one of which is water.Our experiments, theory, and simulations provide evidence that a junctionof two aqueous interfaces (e.g., liquid-solid and liquid-air)develops a pH-dependent contact potential difference Delta phi due to the longitudinal charge redistribution between two contactinginterfaces. This universal static charging mechanism may have implicationsfor the origin of electrical potentials in biological, nanofluidic,and electrochemical systems and helps to predict and control the surfacecharge of water in various experimental environments.

The Three-Phase Contact Potential Difference Modulates the Water Surface Charge

V. Artemov; L. Frank; R. Doronin; P. Staerk; A. Schlaich et al. 

The surface charge of an open water surface is crucialfor solvationphenomena and interfacial processes in aqueous systems. However, themagnitude of the charge is controversial, and the physical mechanismof charging remains incompletely understood. Here we identify a previouslyoverlooked physical mechanism determining the surface charge of water.Using accurate charge measurements of water microdrops, we demonstratethat the water surface charge originates from the electrostatic effectsin the contact line vicinity of three phases, one of which is water.Our experiments, theory, and simulations provide evidence that a junctionof two aqueous interfaces (e.g., liquid-solid and liquid-air)develops a pH-dependent contact potential difference Delta phi due to the longitudinal charge redistribution between two contactinginterfaces. This universal static charging mechanism may have implicationsfor the origin of electrical potentials in biological, nanofluidic,and electrochemical systems and helps to predict and control the surfacecharge of water in various experimental environments.

Optical imaging of the small intestine immune compartment across scales

A. L. Planchette; C. Schmidt; O. Burri; M. G. de Agueero; A. Radenovic et al. 

A workflow for 3D characterization of the mouse small intestine with optical projection tomography allows the identification of sparsely-distributed regions of interest in large volumes while retaining compatibility with high-resolution microscopy modalities.

Disentangling 1/f noise from confined ion dynamics

P. Robin; M. Lizee; Q. Yang; T. Emmerich; A. Siria et al. 

Ion transport through biological and solid-state nanochannels is known to be a highly noisy process. The power spectrum of current fluctuations is empirically known to scale like the inverse of frequency, following the long-standing yet poorly understood Hooge’s law. Here, we report measurements of current fluctuations across nanometer-scale two-dimensional channels with different surface properties. The structure of fluctuations is found to depend on the channel’s material. While in pristine channels current fluctuations scale like 1/f(1+a) with a = 0-0.5, the noise power spectrum of activated graphite channels displays different regimes depending on frequency. Based on these observations, we develop a theoretical formalism directly linking ion dynamics and current fluctuations. We predict that the noise power spectrum takes the form 1/f x S-channel(f), where 1/f fluctuations emerge in fluidic reservoirs on both sides of the channel and S-channel describes fluctuations inside it. Deviations to Hooge’s law thus allow direct access to the ion transport dynamics of the channel – explaining the entire phenomenology observed in experiments on 2D nanochannels. Our results demonstrate how current fluctuations can be used to characterize nanoscale ion dynamics.

High durability and stability of 2D nanofluidic devices for long-term single-molecule sensing

M. Thakur; N. Cai; M. Zhang; Y. Teng; A. Chernev et al. 

Nanopores in two-dimensional (2D) membranes hold immense potential in single-molecule sensing, osmotic power generation, and information storage. Recent advances in 2D nanopores, especially on single-layer MoS2, focus on the scalable growth and manufacturing of nanopore devices. However, there still remains a bottleneck in controlling the nanopore stability in atomically thin membranes. Here, we evaluate the major factors responsible for the instability of the monolayer MoS2 nanopores. We identify chemical oxidation and delamination of monolayers from their underlying substrates as the major reasons for the instability of MoS2 nanopores. Surface modification of the substrate and reducing the oxygen from the measurement solution improves nanopore stability and dramatically increases their shelf-life. Understanding nanopore growth and stability can provide insights into controlling the pore size, shape and can enable long-term measurements with a high signal-to-noise ratio and engineering durable nanopore devices.

Type I IFNs link skin-associated dysbiotic commensal bacteria to pathogenic inflammation and angiogenesis in rosacea

A. Mylonas; H. C. Hawerkamp; Y. Wang; J. Chen; F. Messina et al. 

Rosacea is a common chronic inflammatory skin disease with a fluctuating course of excessive inflammation and apparent neovascularization. Microbial dysbiosis with a high density of Bacillus oleronius and increased activity of kallikrein 5, which cleaves cathelicidin antimicrobial peptide, are key pathogenic triggers in rosacea. However, how these events are linked to the disease remains unknown. Here, we show that type I IFNs produced by plasmacytoid DCs represent the pivotal link between dysbiosis, the aberrant immune response, and neovascularization. Compared with other commensal bacteria, B. oleronius is highly susceptible and preferentially killed by cathelicidin antimicrobial peptides, leading to enhanced generation of complexes with bacterial DNA. These bacterial DNA complexes but not DNA complexes derived from host cells are required for cathelicidin-induced activation of plasmacytoid DCs and type I IFN production. Moreover, kallikrein 5 cleaves cathelicidin into peptides with heightened DNA binding and type I IFN-inducing capacities. In turn, excessive type I IFN expression drives neoangiogenesis via IL-22 induction and upregulation of the IL-22 receptor on endothelial cells. These findings unravel a potentially novel pathomechanism that directly links hallmarks of rosacea to the killing of dysbiotic commensal bacteria with induction of a pathogenic type I IFN-driven and IL-22-mediated angiogenesis.

Imaging of interactions of biomolecules with nanomaterials with interferometric scattering microscopy

J. Sulzle; W. Yang; Y. Shimoda; E. S. Mayner; M. Macha et al. 

Defect engineering of 2D material for biosensing applications

W. Yang; J. Sulzle; Y. Shimoda; E. Mayner; M. Macha et al.