Real-time single-molecule imaging of oxidation catalysis at a liquid-solid interface

Many chemical reactions are catalysed by metal complexes, and insight into their mechanisms is essential for the design of future catalysts. A variety of conventional spectroscopic techniques are available for the study of reaction mechanisms at the ensemble level, and, only recently, fluorescence microscopy techniques have been applied to monitor single chemical reactions carried out on crystal faces and by enzymes. With scanning tunnelling microscopy (STM) it has become possible to obtain, during chemical reactions, spatial information at the atomic level. The majority of these STM studies have been carried out under ultrahigh vacuum, far removed from conditions encountered in laboratory processes. Here we report the single-molecule imaging of oxidation catalysis by monitoring, with STM, individual manganese porphyrin catalysts, in real time, at a liquid-solid interface. It is found that the oxygen atoms from an O2 molecule are bound to adjacent porphyrin catalysts on the surface before their incorporation into an alkene substrate.     

Dissecting contact mechanics from quantum interference in single-molecule junctions of stilbene derivatives

Electronic factors in molecules such as quantum interference and cross-conjugation can lead to dramatic modulation and suppression of conductance in single-molecule junctions. Probing such effects at the single-molecule level requires simultaneous measurements of independent junction properties, as conductance alone cannot provide conclusive evidence of junction formation for molecules with low conductivity. Here, we compare the mechanics of the conducting para-terminated 4,4'-di(methylthio)stilbene and moderately conducting 1,2-bis(4-(methylthio)phenyl)ethane to that of insulating meta-terminated 3,3'-di(methylthio)stilbene single-molecule junctions. We simultaneously measure force and conductance across single-molecule junctions and use force signatures to obtain independent evidence of junction formation and rupture in the meta-linked cross-conjugated molecule even when no clear low-bias conductance is measured. By separately quantifying conductance and mechanics, we identify the formation of atypical 3,3'-di(methylthio)stilbene molecular junctions that are mechanically stable but electronically decoupled. While theoretical studies have envisaged many plausible systems where quantum interference might be observed, our experiments provide the first direct quantitative study of the interplay between contact mechanics and the distinctively quantum mechanical nature of electronic transport in single-molecule junctions.     

Real-time single-molecule kinetics of trypsin proteolysis

Single-molecule enzymatic kinetics and enantioselectivity were monitored in real time by using total internal reflection fluorescence microscopy. The 300-kDa poly(L-lysine) (PLL) or poly(D-lysine) (PDL) was labeled with Alexa Fluor 532 and was covalently immobilized on a dithiobis(succinimidyl undecanoate) self-assembled monolayer (DSU SAM) prepared on a gold substrate. The PLL/PDL chains were more accessible to trypsin on DSU SAM than when they were immobilized on a bare glass substrate. Short-chain PDL was further used as a blocking agent to prevent readsorption of the hydrolyzed lysine fragments. Chain shortening due to enzymatic hydrolysis resulted in the reduction of the individual fluorescence intensities. A broad distribution was obtained when 100 single-molecule half-lives were analyzed. However, the detailed hydrolysis process involved also a long-lived component and an induction period that varied significantly among molecules. Charge and steric heterogeneity at the surface are responsible for these features. In contrast, standard Michaelis-Menten fitting of the decrease in molecule numbers with time masked out all such details.     

Real-time imaging of single-molecule fluorescence with a zero-mode waveguide for the analysis of protein-protein interaction

Real-time imaging of single-molecule fluorescence with a zero-mode waveguide (ZMW) was achieved. With modification of the ZMW geometry, the signal-to-background ratio is twice that obtainable with a conventional ZMW. The improved signal-to-background ratio makes it possible to visualize individual binding-release events between chaperonin GroEL and cochaperonin GroES at a concentration of 5 microM. Two rate constants representing two-timer kinetics in the release of GroES from GroEL were measured with the ZMW, and the measurements agreed well with those made with a total internal reflection fluorescence microscopy. These results indicate that the novel ZMW makes feasible the direct observation of protein-protein interaction at an intracellular concentration in real time.     

Real-time conductivity analysis through single-molecule electrical junctions

Conductance through single-molecule junctions, consisting of nanoparticle/molecule/nanoparticle units between nanoscale planar electrodes, was monitored in real time during several process sequences, including dielectrophoretic directed self-assembly and post-assembly modification. Assembly faults are directly detected in real time when non-ideal assembly conditions result in molecular junction failure and nanoparticle fusion in the junction. The real-time conductivity measured through the junction was sensitive to ambient conditions, and changes persisted over several days of exposure. Atomic layer deposition of Al(2)O(3) was used to encapsulate and isolate the molecular junctions, and the effect of the deposition process sequence on current through the junction was evaluated in real time. Results indicate that the current measured during atomic layer deposition is sensitive to the chemical oxidation and reduction reactions proceeding in the 1-2?nm confined region between assembled nanoparticles.     

DNA-templated protein arrays for single-molecule imaging

Single-particle electron cryomicroscopy permits structural characterization of noncrystalline protein samples, but throughput is limited by problems associated with sample preparation and image processing. Three-dimensional density maps are reconstructed from high resolution but noisy images of individual molecules. We show that self-assembled DNA nanoaffinity templates can create dense, nonoverlapping arrays of protein molecules, greatly facilitating data collection. We demonstrate this technique using a G-protein-coupled membrane receptor, a soluble G-protein, and a signaling complex of both molecules.     

Josephson quantum interference computer devices

Josephson devices are potential elements for ultra-fast computers. Rather complex logic and memory circuits have been realized. Here quantum interference devices with improved speed and power performance are discussed. Latching and non-latching logic operation is possible and experiments with non-latching circuits are reviewed. Memory applications of quantum interference devices are also considered.     

Toward graphene-based quantum interference devices

A new type of quantum interference device based on a graphene nanoring in which all edges are of the same type is studied theoretically. The superposition of the electron wavefunction propagating from the source to the drain along the two arms of the nanoring gives rise to interesting interference effects. We show that a side-gate voltage applied across the ring allows for control of the interference pattern at the drain. The electron current between the two leads can therefore be modulated by the side gate. The latter manifests itself as conductance oscillations as a function of the gate voltage. We study quantum nanorings with two edge types (zigzag or armchair) and argue that the armchair type is more advantageous for applications. We demonstrate finally that our proposed device operates as a quantum interference transistor with high on/off ratio.     

The quantum interference effect transistor

We give a detailed discussion of the quantum interference effect transistor (QuIET), a proposed device which exploits the interference between electron paths through aromatic molecules to modulate the current flow. In the off state, perfect destructive interference stemming from the molecular symmetry blocks the current, while in the on state, the current is allowed to flow by locally introducing either decoherence or elastic scattering. Details of a model calculation demonstrating the efficacy of the QuIET are presented, and various fabrication scenarios are proposed, including the possibility of using conducting polymers to connect the QuIET with multiple leads.     

Nanogel surface coatings for improved single-molecule imaging substrates

Surfaces that resist protein adsorption are important for many bioanalytical applications. Bovine serum albumin (BSA) coatings and multi-arm poly(ethylene glycol) (PEG) coatings display low levels of non-specific protein adsorption and have enabled highly quantitative single-molecule (SM) protein studies. Recently, a method was developed for coating a glass with PEG–BSA nanogels, a promising hybrid of these two low-background coatings. We characterized the nanogel coating to determine its suitability for SM protein experiments. SM adsorption counting revealed that nanogel-coated surfaces exhibit lower protein adsorption than covalently coupled BSA surfaces and monolayers of multi-arm PEG, so this surface displays one of the lowest degrees of protein adsorption yet observed. Additionally, the nanogel coating was resistant to DNA adsorption, underscoring the utility of the coating across a variety of SM experiments. The nanogel coating was found to be compatible with surfactants, whereas the BSA coating was not. Finally, applying the coating to a real-world study, we found that single ligand molecules could be tethered to this surface and detected with high sensitivity and specificity by a digital immunoassay. These results suggest that PEG–BSA nanogel coatings will be highly useful for the SM analysis of proteins.     

Real-time rectilinear volumetric imaging

Current real-time volumetric scanners use a 2-D array to scan a pyramidal volume consisting of many sector scans stacked in the elevation direction. This scan format is primarily useful for cardiac imaging to avoid interference from the ribs. However, a real-time rectilinear volumetric scan with a wider field of view close to the transducer could prove more useful for abdominal, breast, or vascular imaging. In previous work, computer simulations of very sparse array transducer designs in a rectilinear volumetric scanner demonstrated that a Mills cross array showed the best overall performance given current system constraints. Consequently, a 94×94 Mills cross array including 372 active channels operating at 5 MHz has been developed on a flexible circuit interconnect. In addition, the beam former delay software and scan converter display software of the Duke volumetric scanner were modified to achieve real-time rectilinear volumetric scanning consisting of a 30-mm×8-mm×60-mm scan at a rate of 47 volumes/s. Real-time rectilinear volumetric images were obtained of tissue-mimicking phantoms, showing a spatial resolution of 1 to 2 mm. Images of carotid arteries in normal subjects demonstrated tissue penetration to 6 cm     

Carbon nanotube superconducting quantum interference device

A superconducting quantum interference device (SQUID) with single-walled carbon nanotube (CNT) Josephson junctions is presented. Quantum confinement in each junction induces a discrete quantum dot (QD) energy level structure, which can be controlled with two lateral electrostatic gates. In addition, a backgate electrode can vary the transparency of the QD barriers, thus permitting change in the hybridization of the QD states with the superconducting contacts. The gates are also used to directly tune the quantum phase interference of the Cooper pairs circulating in the SQUID ring. Optimal modulation of the switching current with magnetic flux is achieved when both QD junctions are in the 'on' or 'off' state. In particular, the SQUID design establishes that these CNT Josephson junctions can be used as gate-controlled pi-junctions; that is, the sign of the current-phase relation across the CNT junctions can be tuned with a gate voltage. The CNT-SQUIDs are sensitive local magnetometers, which are very promising for the study of magnetization reversal of an individual magnetic particle or molecule placed on one of the two CNT Josephson junctions.     

Excitonic quantum interference in a quantum dot chain with rings

We demonstrate excitonic quantum interference in a closely spaced quantum dot chain with nanorings. In the resonant dipole-dipole interaction model with direct diagonalization method, we have found a peculiar feature that the excitation of specified quantum dots in the chain is completely inhibited, depending on the orientational configuration of the transition dipole moments and specified initial preparation of the excitation. In practice, these excited states facilitating quantum interference can provide a conceptual basis for quantum interference devices of excitonic hopping.     

Damped quantum interference using stochastic calculus

Abstract

It is shown how the phase-damping master equation, either in Markovian and non-Markovian regimes, can be obtained as an averaged random unitary evolution. This, apart from offering a common mathematical set-up for both regimes, enables us to solve this equation in a straightforward manner just by solving the Schrödinger equation and taking the stochastic expectation value of its solutions after an adequate modification. Using the linear entropy as a figure of merit (basically the loss of quantum coherence) four distinct kinds of environment are suggested.     

Electrophoretic quantitation of nucleic acids without amplification by single-molecule imaging

We have developed a novel high-performance quantitative assay for unamplified nucleic acids that is based on single-molecule imaging. The apparatus is a simple but highly sensitive single-molecule detection system that uses a normal CCD camera instead of an image-intensified CCD camera. After the DNA molecules in a sample were labeled with YOYO-1, they were induced to migrate electrophoretically in a polymer solution and imaged. No chemical or biochemical amplification was required. Direct quantitation of the sample by counting molecules was possible, because the number counted over the measurement period was directly proportional to the concentration of DNA molecules in the sample. Nonspecifically labeled impurities that would degrade the sensitivity of the assay were successfully reduced and discriminated from the DNA molecules by differences in electrophoretic mobility. By using beta-actin DNA (838 bp) as a model sample, we demonstrate that this protocol was fast (10-min measurement period), highly sensitive (limit of quantitation: approximately 10(3) copies/sample, or 3 x 10(-16) M), quantitative, and covered a wide linear dynamic range (approximately 10(4)). This high-performance assay promises to be a powerful technology for the quantitation of specific varieties of mRNA in the study of gene functions and diseases and in the clinical detection of mutant cells.     

A quantum loop in magnetic field and a quantum interference rectifier

The electron transport in a curvilinear quantum wire exposed to a magnetic field was studied. A possible design of the quantum interference rectifier is suggested.     

Real-time imaging of astrocyte response to quantum dots: in vivo screening model system for biocompatibility of nanoparticles

Astrocytes are the principle macroglial brain cells. They are activated by different stressors and brain injuries. Quantum dots (QDs) can cause oxidative stress. This study shows a real-time imaging of primary cortical cultures and assessment of QD-induced activation of astrocytes in the brains of transgenic mice with the luciferase gene driven by the murine astrocyte promoter. This approach may be widely applicable for assessing the astroglia/tissue response to nanoparticles in live animals.     

Wide-field-of-view polarization interference imaging spectrometer

A wide-field-of-view polarization interference imaging spectrometer (WPIIS) based on a modified Savart polariscope, without moving parts, and with a narrow slit has been designed. The primary feature of this device is for use with a large angle of incidence, and the target image as well as the interferogram can be obtained at the same time in the spatial domain and are recorded by a two-dimensional CCD camera. Under compensation, the field of view of the WPIIS will extend 3-5 times as large as a common interference imaging spectrometer, and throughput will raise 1-2 orders of magnitude. The developed optics is 20 x 8 cm ? in size. The spectral resolution of the prototype system is 86.8 cm(-1) between 22222.2 and 11111.1 cm(-1). This system has the advantages of being static and ultracompact with wide field of view and a very high throughput. The optics system and especially the wide-field-of-view compensation principle are described, and the experimental result of the interference imaging spectrum is shown.     

Spin-orbit coupling induced interference in quantum corrals

Lack of inversion symmetry at a metallic surface can lead to an observable spin-orbit interaction. For certain metal surfaces, such as the Au(111) surface, the experimentally observed spin-orbit coupling results in spin rotation lengths on the order of tens of nanometers, which is the typical length scale associated with quantum corral structures formed on metal surfaces. In this work, multiple scattering theory is used to calculate the local density of states (LDOS) of quantum corral structures composed of nonmagnetic adatoms in the presence of spin-orbit coupling. Contrary to previous theoretical predictions, spin-orbit coupling induced modulations are observed in the theoretical LDOS, which should be observable using scanning tunneling microscopy.