High-precision high-speed nanopore ping-pong control system based on field programmable gate array.

"Molecular ping-pong," emerging as a control strategy in solid-state nanopore technology, presents a highly promising approach for repetitive measurements of single biomolecules, such as DNA. This paper introduces a high-precision, high-speed nanopore molecular ping-pong control system consisting of a home-built trans-impedance amplifier (TIA), a control system based on a Field Programmable Gate Array (FPGA), and a LabVIEW program operating on the host personal computer. Through feedback compensation and post-stage boosting, the TIA achieves a high bandwidth of about 200 kHz with a gain of 100 MΩ, along with low input-referred current noise of 1.6 × 10-4 pA2/Hz at 1 kHz and 1.1 × 10-3 pA2/Hz at 100 kHz. The FPGA-based control system demonstrates a minimum overall response time (tdelay) of 6.5 µs from the analog input current signal trigger to the subsequent reversal of the analog output drive voltage signal, with a control precision of 1 µs. Additionally, a LabVIEW program has been developed to facilitate rapid data exchange and communication with the FPGA program, enabling real-time signal monitoring, parameter adjustment, and data storage. Successful recapture of individual DNA molecules at various tdelay, resulting in an improvement in capture rate by up to 2 orders of magnitude, has been demonstrated. With unprecedented control precision and capture efficiency, this system provides robust technical support and opens novel research avenues for nanopore single-molecule sensing and manipulation.

Large negative differential conductance and its transformation in a single radical molecule.

The discovery of negative differential conductance (NDC) in a single molecule and mechanism controlling this phenomenon are important for molecular electronics. We investigated the electronic properties of a typical radical molecule 3-carbamoyl-2,2,5,5-tetramethyl-3-pyrrolin-1-yloxy (CTPO) on an Au(111) surface using low-temperature scanning tunneling microscopy (STM) and inelastic electron tunneling spectroscopy. Large NDC was observed in single CTPO molecules at the boundary of the crystal monolayer. The origin of observed NDC is revealed as the inelastic electron-phonon scattering during tunneling, and the strong spatial variation of the NDC over the single molecule illustrates the nature of the localized radical group. In addition, the NDC can be transformed into a positive differential conductance peak by tuning coupling strengths between different tunneling channels. An empirical multi-channel model has been developed to describe the competition between the valley-shaped NDC and peak-shaped positive differential conductance. The unique electronic property and giant conductance change observed in this radical molecule is valuable for designing novel molecular devices in the future.

Geometrical and magnetic properties of small titanium and chromium clusters on monolayer hexagonal boron nitride.

Magnetic clusters on an insulating substrate are potential candidates for spin-based quantum devices. Here we investigate the geometric, electronic, and magnetic structures of small Ti and Cr clusters, from dimers to pentamers, adsorbed on a single-layer hexagonal boron nitride (h-BN) sheet within the framework of density functional theory. The stable adsorption configurations of the Ti clusters and Cr clusters composed of the same number of atoms are found to be totally different from each other. The difference in their bonding mechanisms has been revealed by the density of states and the charge density difference of the corresponding adsorption systems. While chemical bonds are formed between the Ti atoms and the supporting sheet, the Cr clusters are found in the physisorption state on the substrate. In addition, it is shown that the h-BN sheet is energetically favorable for building three-dimensional Ti clusters. These findings support the use of h-BN as a suitable decoupling substrate for manipulation of quantum spin states in small transition metal (TM) clusters and fabrication of devices based on them.

Spatially Resolved Stimulation for the Controlled Debromination in Single Molecules on a Surface.

A controlled chemical reaction on a specific bond in a single molecule is an inevitable step toward atomic engineering and fabrication. Here, we explored the debromination of a single 9,10-dibromoanthracene (DBA) molecule on a surface as stimulated by the voltage pulse through the tip of a scanning tunneling microscope (STM). A voltage threshold of about 2.2 V is obtained, and the nature of single-electron process is revealed. The spatially resolved debromination yield is obtained as a function of the pulse magnitude, which presents strong asymmetry for the two C-Br bonds. The optimal stimulation parameters including the pulse magnitude and the tip locations are suggested. The distinct dynamics in dissociation of the two bonds are illustrated by their energy diagrams and recoil paths, as derived by the first-principles density functional theory (DFT) calculation. The influence of the local electric field due to the STM tip on the dissociation of the C-Br bond has also been discussed. The study presents detailed practice for the controlled debromination in a single DBA molecule, which may lead to automated atomic engineering and fabrication of artificial nanostructures in the future.

Ionic Current Fluctuation and Orientation of Tetrahedral DNA Nanostructures in a Solid-State Nanopore.

Understanding the dynamic behavior of a nanostructure translocating through a nanopore is important for various applications. In this paper, the characteristics in ion current traces of tetrahedral DNA nanostructures (TDN) translocating through a solid-state nanopore are examined, by combined experimental and theoretical simulations. The results of finite element analysis reveal the correlation between orientation of TDN and the conductance blockade. The experimentally measured fluctuations in the conductance blockade, expressed as voltage-dependent histogram profiles, are consistent with the simulation, revealing the nature of a random distribution in orientation and weak influence of electrostatic and viscous torques. The step changes in orientation of a TDN during translocation are further explained by the collision with the nanopore, while the gradual changes in orientation illustrate the impact of a weak torque field in the nano-fluidic channel. The results demonstrate a general method and basic understanding in the dynamic behavior of nanostructures translocating through solid-state nanopores.

Edge-Enriched Large-Area Hexagonal BN Ultrathin Films with Enhanced Optical Second Harmonic Generation.

The optical second harmonic generation (SHG) efficiency of hexagonal boron nitride (h-BN) layered materials is profoundly influenced by the symmetry properties, which has severely limited the usefulness of their SHG for nonlinear optical applications. Herein, we report on the controlled growth of large-area and continuous ultrathin h-BN films with a high density of exposed edges that show strongly enhanced SHG, owing to the breaking of inversion symmetry occurring naturally at edge sites. The large-area growth of edge-enriched BN films was accomplished through the introduction of Turing instability into a growth process that involves the liquid-gas interface self-limiting reaction between molten boron oxide (B2O3) with gaseous ammonia (NH3) at elevated temperature. Remarkably, the edge-enriched BN films give rise to a SHG response up to nearly 3 orders of magnitude higher than that of the smooth BN films prepared through the same growth approach but with different growth parameters.

Detection and Characterization of Single Cisplatin Adducts on DNA by Nanopore Sequencing.

Detection and characterization of an individual cisplatin adduct on a single DNA molecule is a demanding task. We explore the characteristic features of cisplatin adducts in the nanopore sequencing signal in aspects of dwell time, genome anchored current trace, and basecalling accuracy. The offset between the motor protein and the nanopore constriction region is revealed by dwell time analysis to be about 14 bases in the nanopore device as we examined. Characteristic distortions due to cisplatin adducts are illustrated in genome anchored current trace analysis, constituting the fingerprint for identification of cisplatin adduct. The sharp increase in odds ratio at the location of adducting sites provides additional feature in the detection of the adduct. By these combined methods, single cisplatin adducts can be detected with high fidelity on a single read of the DNA sequence. The study demonstrates an effective method in the detection and characterization of single cisplatin adducts on DNA at the single-molecule level and with single nucleotide spatial resolution.

Revealing Differential Interaction Forces during Nanopore DNA Sequencing.

The interaction between DNA and the nanopore structure plays an important role in nanopore DNA sequencing. Differential interaction forces between each base type and the nanopore structure are obtained by examining the correlation between translocation dwell time and the sequence. The viscous drag force and the intermolecular interaction are identified with single-nucleotide resolution. Active hydrogen donors and acceptors on the inner wall of the nanopore structure are revealed at various offset coordinates. The differential forces as demonstrated in this study have great potential in probing active hydrogen bond interaction in a single protein molecule with subnanometer spatial resolution.

Orientation Switching of Single Molecules on Surface Excited by Tunneling Electrons and Ultrafast Laser Pulses.

We investigate the orientation switching of individual azobenzene molecules adsorbed on a Au(111) surface using a laser-assisted scanning tunneling microscope (STM). It is found that the rotational motion of the molecule can be regulated by both sample bias and laser wavelength. By measuring the switching rate and state occupation as a function of both bias voltage and photon energy, the threshold in sample bias and the minimal photon energy are derived. It has been revealed that the tip-induced local electrostatic potential remarkably contributes to the reduction in hopping barrier. We also find that the tunneling electrons and photons play distinct roles in controlling rotational dynamics of single azobenzene molecules on the surface, which are useful for understanding dynamic behaviors in similar molecular systems.

Rotational and Vibrational Excitations of a Single Water Molecule by Inelastic Electron Tunneling Spectroscopy.

Two low-energy excitations of a single water molecule are observed via inelastic electron tunneling spectroscopy, where a significant enhancement is achieved by attaching the molecule to the tip apex in a scanning tunneling microscope. Density functional theory simulations and quantum mechanical calculations of an asymmetric top are carried out to reveal the origin of both excitations. Variations in tunneling junction separation give rise to the quantum confinement effect on the quantum state of a water molecule in the tunneling junction. Our results demonstrate a potential method for measuring the dynamic behavior of a single molecule confined in a tunneling junction, where the molecule-substrate interaction can be purposely tuned.

Charge-Transfer-Induced Photoluminescence Properties of WSe2 Monolayer-Bilayer Homojunction.

The charge-transfer process in transition-metal dichalcogenides (TMDCs) lateral homojunction affects the electron-hole recombination process of in optoelectronic devices. However, the optical properties of the homojunction reflecting the charge-transfer process has not been observed and studied. In this work, we investigated the charge-transfer-induced emission properties based on monolayer (1L)-bilayer (2L) WSe2 lateral homojunction with dozens of nanometer monolayer region. On the one hand, the photoluminescence (PL) emission of bilayer WSe2 from the homojunction area blue shifts ∼23 and ∼31 meV for direct and indirect bandgap emission, respectively, compared with the bare WSe2 bilayer region. The blue shift of the emission spectrum in the bilayer WSe2 is ascribed to the decrease in binding energy induced by charge transfer from monolayer to bilayer. On the other hand, the energy shift shows a tendency to increase as the temperature decreases. The energy blue shift is ∼57 meV for direct bandgap emission at 80 K, which is larger than that (∼23 meV) at room temperature. The larger-energy blue shift at low temperature is derived from the larger driving force under larger band offset. Our observations of the unique optical properties induced by efficient charge transfer are very helpful for exploring novel TMDC-based optoelectronic devices.

Translocation of tetrahedral DNA nanostructures through a solid-state nanopore.

Tetrahedral DNA nanostructures (TDNs) are programmable DNA nanostructures that have great potential in bio-sensing, cell imaging and therapeutic applications. In this study, we investigate the translocation behavior of individual TDNs through solid-state nanopores. Pronounced translocation signals for TDNs are observed that are sensitive to the size of the nanostructures. TDNs bound to linear DNA molecules produce an extra signal in the ionic current traces. Statistical analysis of its relative temporal position reveals distinct features between TDNs bound to the end and those bound to the middle of the linear DNA molecules. A featured current trace for two TDNs bound to the same linear DNA molecule has also been observed. Our study demonstrates the potential of using TDNs as sensitive bio-sensors to detect specific segments of a single DNA molecule in real time, based on solid-state nanopore devices.

Identifying Few-Molecule Water Clusters with High Precision on Au(111) Surface.

Revealing the nature of a hydrogen-bond network in water structures is one of the imperative objectives of science. With the use of a low-temperature scanning tunneling microscope, water clusters on a Au(111) surface were directly imaged with molecular resolution by a functionalized tip. The internal structures of the water clusters as well as the geometry variations with the increase of size were identified. In contrast to a buckled water hexamer predicted by previous theoretical calculations, our results present deterministic evidence for a flat configuration of water hexamers on Au(111), corroborated by density functional theory calculations with properly implemented van der Waals corrections. The consistency between the experimental observations and improved theoretical calculations not only renders the internal structures of absorbed water clusters unambiguously, but also directly manifests the crucial role of van der Waals interactions in constructing water-solid interfaces.

Near-Infrared Excitation/Emission and Multiphoton-Induced Fluorescence of Carbon Dots.

Carbon dots (CDs) have significant potential for use in various fields including biomedicine, bioimaging, and optoelectronics. However, inefficient excitation and emission of CDs in both near-infrared (NIR-I and NIR-II) windows remains an issue. Solving this problem would yield significant improvement in the tissue-penetration depth for in vivo bioimaging with CDs. Here, an NIR absorption band and enhanced NIR fluorescence are both realized through the surface engineering of CDs, exploiting electron-acceptor groups, namely molecules or polymers rich in sulfoxide/carbonyl groups. These groups, which are bound to the outer layers and the edges of the CDs, influence the optical bandgap and promote electron transitions under NIR excitation. NIR-imaging information encryption and in vivo NIR fluorescence imaging of the stomach of a living mouse using CDs modified with poly(vinylpyrrolidone) in aqueous solution are demonstrated. In addition, excitation by a 1400 nm femtosecond laser yields simultaneous two-photon-induced NIR emission and three-photon-induced red emission of CDs in dimethyl sulfoxide. This study represents the realization of both NIR-I excitation and emission as well as two-photon- and three-photon-induced fluorescence of CDs excited in an NIR-II window, and provides a rational design approach for construction and clinical applications of CD-based NIR imaging agents.

Laser Thinning and Patterning of MoS2 with Layer-by-Layer Precision.

The recently discovered novel properties of two dimensional materials largely rely on the layer-critical variation in their electronic structure and lattice symmetry. Achieving layer-by-layer precision patterning is thus crucial for junction fabrications and device engineering, which hitherto poses an unprecedented challenge. Here we demonstrate laser thinning and patterning with layer-by-layer precision in a two dimensional (2D) quantum material MoS2. Monolayer, bilayer and trilayer of MoS2 films are produced with precise vertical and lateral control, which removes the extruding barrier for fabricating novel three dimensional (3D) devices composed of diverse layers and patterns. By tuning the laser fluence and exposure time we demonstrate producing MoS2 patterns with designed layer numbers. The underlying physics mechanism is identified to be temperature-dependent evaporation of the MoS2 lattice, verified by our measurements and calculations. Our investigation paves way for 3D device fabrication based on 2D layered quantum materials.

Revealing Three Stages of DNA-Cisplatin Reaction by a Solid-State Nanopore.

The dynamic structural behavior in DNA due to interaction with cisplatin is essential for the functionality of platinum-based anti-cancer drugs. Here we report a novel method to monitor the interaction progress in DNA-cisplatin reaction in real time with a solid-state nanopore. The interaction processes are found to be well elucidated by the evolution of the capture rate of DNA-cisplatin complex, which is defined as the number of their translocation events through the nanopore in unit time. In the first stage, the capture rate decreases rapidly due to DNA discharging as the positive-charged hydrated cisplatin molecules initially bond to the negative-charged DNA and form mono-adducts. In the second stage, by forming di-adducts, the capture rate increases as DNA molecules are softened, appears as the reduced persistence length of the DNA-cisplatin adducts. In the third stage, the capture rate decreases again as a result of DNA aggregation. Our study demonstrates a new single-molecule tool in exploring dynamic behaviors during drug-DNA reactions and may have future application in fast drug screening.

Precise identification and manipulation of adsorption geometry of donor-π-acceptor dye on nanocrystalline TiO2 films for improved photovoltaics.

Adsorption geometry of dye molecules on nanocrystalline TiO2 plays a central role in dye-sensitized solar cells, enabling effective sunlight absorption, fast electron injection, optimized interface band offsets, and stable photovoltaic performance. However, precise determination of dye binding geometry and proportion has been challenging due to complexity and sensitivity at interfaces. Here employing combined vibrational spectrometry and density functional calculations, we identify typical adsorption configurations of widely adopted cyanoacrylic donor-π bridge-acceptor dyes on nanocrystalline TiO2. Binding mode switching from bidentate bridging to hydrogen-bonded monodentate configuration with Ti-N bonding has been observed when dye-sensitizing solution becomes more basic. Raman and infrared spectroscopy measurements confirm this configuration switch and determine quantitatively the proportion of competing binding geometries, with vibration peaks assigned using density functional theory calculations. We further found that the proportion of dye-binding configurations can be manipulated by adjusting pH value of dye-sensitizing solutions. Controlling molecular adsorption density and configurations led to enhanced energy conversion efficiency from 2.4% to 6.1% for the fabricated dye-sensitized solar cells, providing a simple method to improve photovoltaic performance by suppressing unfavorable binding configurations in solar cell applications.

DNA translocation through hydrophilic nanopore in hexagonal boron nitride.

Ultra-thin solid-state nanopore with good wetting property is strongly desired to achieve high spatial resolution for DNA sequencing applications. Atomic thick hexagonal boron nitride (h-BN) layer provides a promising two-dimensional material for fabricating solid-state nanopores. Due to its good oxidation resistance, the hydrophilicity of h-BN nanopore device can be significantly improved by UV-Ozone treatment. The contact angle of a KCl-TE droplet on h-BN layer can be reduced from 57° to 26° after the treatment. Abundant DNA translocation events have been observed in such devices, and strong DNA-nanopore interaction has been revealed in pores smaller than 10 nm in diameter. The 1/f noise level is closely related to the area of suspended h-BN layer, and it is significantly reduced in smaller supporting window. The demonstrated performance in h-BN nanopore paves the way towards base discrimination in a single DNA molecule.

Turning on and off the rotational oscillation of a single porphine molecule by molecular charge state.

The rotation dynamics of single magnesium porphine molecules on an ultrathin NaCl bilayer is investigated with low-temperature scanning tunneling microscopy and density functional theory calculations. It is observed that the rotational oscillation between two stable orientations can be turned on and off by the molecular charge state, which can be manipulated with the tunneling electrons. The features of the charge states and the mechanism of molecular rotational on/off state control are revealed at the atomic scale. The dependence of molecular orientation switching rate on the tunneling electron energy and the current density illustrates the underlying resonant tunneling excitation and single-electron process. The drive and control of molecular motion with tunneling electrons demonstrated in this study suggests a novel approach toward electronically controlled molecular rotors and motors.

Modulating resonance modes and Q value of a CdS nanowire cavity by single Ag nanoparticles.

Semiconductor nanowire (NW) cavities with tailorable optical modes have been used to develop nanoscale oscillators and amplifiers in microlasers, sensors, and single photon emitters. The resonance modes of NW could be tuned by different boundary conditions. However, continuously and reversibly adjusting resonance modes and improving Q-factor of the cavity remain a great challenge. We report a method to modulate resonance modes continuously and reversibly and improve Q-factor based on surface plasmon-exciton interaction. By placing single Ag nanoparticle (NP) nearby a CdS NW, we show that the wavelength and relative intensity of the resonance modes in the NW cavity can systematically be tuned by adjusting the relative position of the Ag NP. We further demonstrate that a 56% enhancement of Q-factor and an equivalent π-phase shift of the resonance modes can be achieved when the Ag NP is located near the NW end. This hybrid cavity has potential applications in active plasmonic and photonic nanodevices.