Single-molecule characterization of a bright and photostable deep-red fluorescent squaraine-figure-eight (SF8) dye.

Squaraine Figure Eight (SF8) dyes are a unique class of deep-red fluorescent dyes with self-threaded molecular architecture that provides structural rigidity while simultaneously encapsulating and protecting the emissive fluorochrome. Previous cell microscopy and bulk phase studies of SF8 dyes indicated order of magnitude enhancements in photostability over conventional pentamethine cyanine dyes such as Cy5. Studies conducted at the single molecule level now reveal that these ensemble level enhancements carry over to the single molecule level in terms of enhanced emission quantum yields, longer times to photobleaching, and enhanced total photon yields. When compared to Cy5, the SF8-based dye SF8(D4)2 possesses a three-fold larger single molecule emission quantum yield, exhibits order of magnitude longer average times before photobleaching, and exhibits twenty times larger photon yields. Additional features such as water solubility, fluorochrome encapsulation to protect it against nucleophilic attack, and selective biomarker targeting capability make SF8-based dyes promising candidates for biological labeling and microscopy applications and single molecule tracking.

Self-Healing Ability of Perovskites Observed via Photoluminescence Response on Nanoscale Local Forces and Mechanical Damage.

The photoluminescence (PL) of metal halide perovskites can recover after light or current-induced degradation. This self-healing ability is tested by acting mechanically on MAPbI3 polycrystalline microcrystals by an atomic force microscope tip (applying force, scratching, and cutting) while monitoring the PL. Although strain and crystal damage induce strong PL quenching, the initial balance between radiative and nonradiative processes in the microcrystals is restored within a few minutes. The stepwise quenching-recovery cycles induced by the mechanical action is interpreted as a modulation of the PL blinking behavior. This study proposes that the dynamic equilibrium between active and inactive states of the metastable nonradiative recombination centers causing blinking is perturbed by strain. Reversible stochastic transformation of several nonradiative centers per microcrystal under application/release of the local stress can lead to the observed PL quenching and recovery. Fitting the experimental PL trajectories by a phenomenological model based on viscoelasticity provides a characteristic time of strain relaxation in MAPbI3 on the order of 10-100 s. The key role of metastable defect states in nonradiative losses and in the self-healing properties of perovskites is suggested.

Are Shockley-Read-Hall and ABC models valid for lead halide perovskites?

Metal halide perovskites are an important class of emerging semiconductors. Their charge carrier dynamics is poorly understood due to limited knowledge of defect physics and charge carrier recombination mechanisms. Nevertheless, classical ABC and Shockley-Read-Hall (SRH) models are ubiquitously applied to perovskites without considering their validity. Herein, an advanced technique mapping photoluminescence quantum yield (PLQY) as a function of both the excitation pulse energy and repetition frequency is developed and employed to examine the validity of these models. While ABC and SRH fail to explain the charge dynamics in a broad range of conditions, the addition of Auger recombination and trapping to the SRH model enables a quantitative fitting of PLQY maps and low-power PL decay kinetics, and extracting trap concentrations and efficacies. However, PL kinetics at high power are too fast and cannot be explained. The proposed PLQY mapping technique is ideal for a comprehensive testing of theories and applicable to any semiconductor.

Mass Spectrometric Identification of Proteins Enhanced by the Atomic Force Microscopy Immobilization Surface.

An approach to highly-sensitive mass spectrometry detection of proteins after surface-enhanced concentrating has been elaborated. The approach is based on a combination of mass spectrometry and atomic force microscopy to detect target proteins. (1) Background: For this purpose, a technique for preliminary preparation of molecular relief surfaces formed as a result of a chemical or biospecific concentration of proteins from solution was developed and tested on several types of chip surfaces. (2) Methods: mass spectrometric identification of proteins using trailing detectors: ion trap, time of flight, orbital trap, and triple quadrupole. We used the electrospray type of ionization and matrix-assisted laser desorption/ionization. (3) Results: It is shown that when using locally functionalized atomically smooth surfaces, the sensitivity of the mass spectrometric method increases by two orders of magnitude as compared with measurements in solution. Conclusions: It has been demonstrated that the effective concentration of target proteins on specially prepared surfaces increases the concentration sensitivity of mass spectrometric detectors-time-of-flight, ion trap, triple quadrupole, and orbital ion trap in the concentration range from up to 10-15 M.

Contribution of electron-phonon coupling to the luminescence spectra of single colloidal quantum dots.

Luminescence spectroscopy experiments were realized for single colloidal quantum dots CdSe/ZnS in a broad temperature range above room temperature in a nitrogen atmosphere. Broadening and shifts of spectra due to the temperature change as well as due to spectral diffusion processes were detected and analyzed. A linear correlation between the positions of maxima and the squared linewidths of the spectra was found. This dependence was explained by a model that takes into account the slow variation of the electron-phonon coupling strength.

Potato Pathogens in Russia's Regions: An Instrumental Survey with the Use of Real-Time PCR/RT-PCR in Matrix Format.

Viral and bacterial diseases of potato cause significant yield loss worldwide. The current data on the occurrence of these diseases in Russia do not provide comprehensive understanding of the phytosanitary situation. Diagnostic systems based on disposable stationary open qPCR micromatrices intended for the detection of eight viral and seven bacterial/oomycetal potato diseases have been used for wide-scale screening of target pathogens to estimate their occurrence in 11 regions of Russia and to assess suitability of the technology for high-throughput diagnostics under conditions of field laboratories. Analysis of 1025 leaf and 725 tuber samples confirmed the earlier reported data on the dominance of potato viruses Y, S, and M in most regions of European Russia, as well as relatively high incidences of Clavibacter michiganensis subsp. sepedonicus, Pectobacterium atrosepticum, and P. carotovorum subsp. carotovorum, and provided detailed information on the phytosanitary status of selected regions and geographical spread of individual pathogens. Information on the occurrence of mixed infections, including their composition, was the first data set of this kind for Russia. The study is the first large-scale screening of a wide range of potato pathogens conducted in network mode using unified methodology and standardized qPCR micromatrices. The data represent valuable information for plant pathologists and potato producers and indicate the high potential of the combined use of matrix PCR technology and network approaches to data collection and analysis with the view to rapidly and accurately assess the prevalence of certain pathogens, as well as the phytosanitary state of large territories.

Detection of hepatitis C virus core protein in serum by atomic force microscopy combined with mass spectrometry.

A method for detection and identification of core antigen of hepatitis C virus (HCVcoreAg)-containing particles in the serum was proposed, with due account taken of the interactions of proteotypic peptides with Na(+), K(+), and Cl(-) ions. The method is based on a combination of reversible biospecific atomic force microscopy (AFM)-fishing and mass spectrometry (MS). AFM-fishing enables concentration, detection, and counting of protein complexes captured on the AFM chip surface, with their subsequent MS identification. Biospecific AFM-fishing of HCVcoreAg-containing particles from serum samples was carried out using AFM chips with immobilized antibodies against HCVcoreAg (HCVcoreAgim). Formation of complexes between anti-HCVcoreAgim and HCVcoreAg-containing particles on the AFM chip surface during the fishing process was demonstrated. These complexes were registered and counted by AFM. Further MS analysis allowed reliable identification of HCVcoreAg within the complexes formed on the AFM chip surface. It was shown that MS data processing, with account taken of the interactions between HCVcoreAg peptides and Na(+), K(+) cations, and Cl(-) anions, allows an increase in the number of peptides identified.

Atomic force microscopy fishing and mass spectrometry identification of gp120 on immobilized aptamers.

Atomic force microscopy (AFM) was applied to carry out direct and label-free detection of gp120 human immunodeficiency virus type 1 envelope glycoprotein as a target protein. This approach was based on the AFM fishing of gp120 from the analyte solution using anti-gp120 aptamers immobilized on the AFM chip to count gp120/aptamer complexes that were formed on the chip surface. The comparison of image contrasts of fished gp120 against the background of immobilized aptamers and anti-gp120 antibodies on the AFM images was conducted. It was shown that an image contrast of the protein/aptamer complexes was two-fold higher than the contrast of the protein/antibody complexes. Mass spectrometry identification provided an additional confirmation of the target protein presence on the AFM chips after biospecific fishing to avoid any artifacts.

Universality of the fluorescence intermittency in nanoscale systems: experiment and theory.

A variety of optically active nanoscale objects show extremely long correlations in the fluctuations of fluorescence intensity (blinking). Here we performed a systematic study to quantitatively estimate the power spectral density (PSD) of the fluorescence trajectories of colloidal and self-assembled quantum dots (QDs), nanorods (NRs), nanowires (NWs), and organic molecules. We report for the first time a statistically correct method of PSD estimation suitable for these systems. Our method includes a detailed analysis of the confidence intervals. The striking similarity in the spectra of these nanoscale systems, including even a "nonblinking" quantum dot investigated by Wang and collaborators (Nature2009, 459, 685-689), is powerful evidence for the existence of a universal physical mechanism underlying the blinking phenomenon in all of these fluorophores (Frantsuzov et al. Nat. Phys.2008, 4, 519-522). In this paper we show that the features of this universal mechanism can be captured phenomenologically by the multiple recombination center model (MRC) we suggested recently for explaining single colloidal QD intermittency. Within the framework of the MRCs we qualitatively explain all of the important features of fluorescence intensity fluctuations for a broad spectrum of nanoscale emitters.

Photoinduced electron transfer from semiconductor quantum dots to metal oxide nanoparticles.

Quantum dot-metal oxide junctions are an integral part of next-generation solar cells, light emitting diodes, and nanostructured electronic arrays. Here we present a comprehensive examination of electron transfer at these junctions, using a series of CdSe quantum dot donors (sizes 2.8, 3.3, 4.0, and 4.2 nm in diameter) and metal oxide nanoparticle acceptors (SnO(2), TiO(2), and ZnO). Apparent electron transfer rate constants showed strong dependence on change in system free energy, exhibiting a sharp rise at small driving forces followed by a modest rise further away from the characteristic reorganization energy. The observed trend mimics the predicted behavior of electron transfer from a single quantum state to a continuum of electron accepting states, such as those present in the conduction band of a metal oxide nanoparticle. In contrast with dye-sensitized metal oxide electron transfer studies, our systems did not exhibit unthermalized hot-electron injection due to relatively large ratios of electron cooling rate to electron transfer rate. To investigate the implications of these findings in photovoltaic cells, quantum dot-metal oxide working electrodes were constructed in an identical fashion to the films used for the electron transfer portion of the study. Interestingly, the films which exhibited the fastest electron transfer rates (SnO(2)) were not the same as those which showed the highest photocurrent (TiO(2)). These findings suggest that, in addition to electron transfer at the quantum dot-metal oxide interface, other electron transfer reactions play key roles in the determination of overall device efficiency.

Correlations between subsequent blinking events in single quantum dots.

We explain the long-range correlations found by Stefani and his co-workers between blinking times of single colloidal quantum dot emission. Our explanation is based on the multiple recombination center model we recently suggested. The model produces positive correlations between subsequent on--on and off--off times and negative on--off correlations, as observed in the experiment. We also reproduce qualitatively the dependence of correlations between subsequent on--on, on-off, and off--off times on the number of switching events separating them.

Model of fluorescence intermittency of single colloidal semiconductor quantum dots using multiple recombination centers.

We present a new physical model resolving a long-standing mystery of the power-law distributions of the blinking times in single colloidal quantum dot fluorescence. The model considers the nonradiative relaxation of the exciton through multiple recombination centers. Each center is allowed to switch between two quasistationary states. We point out that the conventional threshold analysis method used to extract the exponents of the distributions for the on times and off times has a serious flaw: the qualitative properties of the distributions strongly depend on the threshold value chosen for separating the on and off states. Our new model explains naturally this threshold dependence, as well as other key experimental features of the single quantum dot fluorescence trajectories, such as the power-law power spectrum (1/f noise).

Quantum transitions in Lennard-Jones clusters.

The ground states of Lennard-Jones (LJ) clusters are estimated by finding the Gaussian wave packets that minimize the energy functional. A "phase diagram" for LJ_{n} as a function of size (n=31,...,45) and de Boer quantum delocalization length (Lambdain[0;0.3]) is constructed, showing the stability ranges for the two competing structural motifs, the Mackay and anti-Mackay icosahedra. An increase of Lambda has an effect similar to heating and as such may induce structural transformations.

Equilibrium properties of quantum water clusters by the variational Gaussian wavepacket method.

The variational Gaussian wavepacket (VGW) method in combination with the replica-exchange Monte Carlo is applied to calculations of the heat capacities of quantum water clusters, (H(2)O)(8) and (H(2)O)(10). The VGW method is most conveniently formulated in Cartesian coordinates. These in turn require the use of a flexible (i.e., unconstrained) water potential. When the latter is fitted as a linear combination of Gaussians, all the terms involved in the numerical solution of the VGW equations of motion are analytic. When a flexible water model is used, a large difference in the timescales of the inter- and intramolecular degrees of freedom generally makes the system very difficult to simulate numerically. Yet, given this difficulty, we demonstrate that our methodology is still practical. We compare the computed heat capacities to those for the corresponding classical systems. As expected, the quantum effects shift the melting temperatures toward the lower values.

Multiple structural transformations in Lennard-Jones clusters: generic versus size-specific behavior.

The size-temperature "phase diagram" for Lennard-Jones clusters LJn with sizes up to n=147 is constructed based on the analysis of the heat capacities and orientational bond order parameter distributions computed by the exchange Monte Carlo method. Two distinct types of "phase transitions" accompanied by peaks in the heat capacities are proven to be generic. Clusters with Mackay atom packing in the overlayer undergo a lower-temperature melting (or Mackay-anti-Mackay) transition that occurs within the overlayer. All clusters undergo a higher-temperature transition, which for the three-layer clusters is proven to be the 55-atom-core-melting transition. For the two-layer clusters, the core/overlayer subdivision is ambiguous, so the higher-temperature transition is better characterized as the breaking of the local icosahedral coordination symmetry. A pronounced size-specific behavior can typically be observed at low temperatures and often occurs in clusters with highly symmetric global minima. An example of such behavior is LJ135, which undergoes a low-temperature solid-solid transition, besides the two generic transitions, i.e., the overlayer reconstruction and the core melting.

Structural transformations and melting in neon clusters: quantum versus classical mechanics.

The extraordinary complexity of Lennard-Jones (LJ) clusters, which exhibit numerous structures and "phases" when their size or temperature is varied, presents a great challenge for accurate numerical simulations, even without accounting for quantum effects. To study the latter, we utilize the variational Gaussian wave packet method in conjunction with the exchange Monte Carlo sampling technique. We show that the quantum nature of neon clusters has a substantial effect on their size-temperature "phase diagrams," particularly the critical parameters of certain structural transformations. We also give a numerical confirmation that none of the nonicosahedral structures observed for some classical LJ clusters are favorable in the quantum case.

Structural transitions and melting in LJ(74-78) Lennard-Jones clusters from adaptive exchange Monte Carlo simulations.

Phase changes in Lennard-Jones (LJ) clusters containing between 74 and 78 atoms are investigated by means of exchange Monte Carlo simulations in the canonical ensemble. The replica temperatures are self-adapted to facilitate the convergence. Although the 74- and 78-atom clusters have icosahedral global minima, the clusters with 75-77 atoms have decahedral ground-state structures and they undergo a structural transition to icosahedral minima before melting. The structural transitions are characterized by quenching and by looking at the Q4 and Q6 orientational bond order parameters. The transition temperatures are estimated to be 0.114, 0.065, and 0.074 reduced units for LJ75, LJ76, and LJ77, respectively. These values, their ordering and the associated latent heats are compared with other estimates based on the harmonic superposition approach.

Size-temperature phase diagram for small Lennard-Jones clusters.

The size-temperature "phase diagram" for small Lennard-Jones clusters LJn (n< or =147) is constructed based on the analysis of the heat capacities Cv(T) , computed by the parallel tempering Monte Carlo method. Two types of "phase transitions" are often observed: the higher-temperature solid-liquid transition, due to melting of the cluster core, and the lower-temperature melting that occurs within the surface layer. The latter transition can only be observed for clusters with Mackay packing of the overlayer.

Thermodynamics and equilibrium structure of Ne38 cluster: quantum mechanics versus classical.

The equilibrium properties of classical Lennard-Jones (LJ38) versus quantum Ne38 Lennard-Jones clusters are investigated. The quantum simulations use both the path-integral Monte Carlo (PIMC) and the recently developed variational-Gaussian wave packet Monte Carlo (VGW-MC) methods. The PIMC and the classical MC simulations are implemented in the parallel tempering framework. The classical heat capacity Cv(T) curve agrees well with that of Neirotti et al. [J. Chem. Phys. 112, 10340 (2000)], although a much larger confining sphere is used in the present work. The classical Cv(T) shows a peak at about 6 K, interpreted as a solid-liquid transition, and a shoulder at approximately 4 K, attributed to a solid-solid transition involving structures from the global octahedral (Oh) minimum and the main icosahedral (C5v) minimum. The VGW method is used to locate and characterize the low energy states of Ne38, which are then further refined by PIMC calculations. Unlike the classical case, the ground state of Ne38 is a liquidlike structure. Among the several liquidlike states with energies below the two symmetric states (Oh and C5v), the lowest two exhibit strong delocalization over basins associated with at least two classical local minima. Because the symmetric structures do not play an essential role in the thermodynamics of Ne38, the quantum heat capacity is a featureless curve indicative of the absence of any structural transformations. Good agreement between the two methods, VGW and PIMC, is obtained. The present results are also consistent with the predictions by Calvo et al. [J. Chem. Phys. 114, 7312 (2001)] based on the quantum superposition method within the harmonic approximation. However, because of its approximate nature, the latter method leads to an incorrect assignment of the Ne38 ground state as well as to a significant underestimation of the heat capacity.

Quantum statistical mechanics with Gaussians: equilibrium properties of van der Waals clusters.

The variational Gaussian wave-packet method for computation of equilibrium density matrices of quantum many-body systems is further developed. The density matrix is expressed in terms of Gaussian resolution, in which each Gaussian is propagated independently in imaginary time beta=(k(B)T)(-1) starting at the classical limit beta=0. For an N-particle system a Gaussian exp[(r-q)(T)G(r-q)+gamma] is represented by its center qinR(3N), the width matrix GinR(3Nx3N), and the scale gammainR, all treated as dynamical variables. Evaluation of observables is done by Monte Carlo sampling of the initial Gaussian positions. As demonstrated previously at not-very-low temperatures the method is surprisingly accurate for a range of model systems including the case of double-well potential. Ideally, a single Gaussian propagation requires numerical effort comparable to the propagation of a single classical trajectory for a system with 9(N(2)+N)/2 degrees of freedom. Furthermore, an approximation based on a direct product of single-particle Gaussians, rather than a fully coupled Gaussian, reduces the number of dynamical variables to 9N. The success of the methodology depends on whether various Gaussian integrals needed for calculation of, e.g., the potential matrix elements or pair correlation functions could be evaluated efficiently. We present techniques to accomplish these goals and apply the method to compute the heat capacity and radial pair correlation function of Ne(13) Lennard-Jones cluster. Our results agree very well with the available path-integral Monte Carlo calculations.