Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor.

We extend the sensitivity of fluorescence resonance energy transfer (FRET) to the single molecule level by measuring energy transfer between a single donor fluorophore and a single acceptor fluorophore. Near-field scanning optical microscopy (NSOM) is used to obtain simultaneous dual color images and emission spectra from donor and acceptor fluorophores linked by a short DNA molecule. Photodestruction dynamics of the donor or acceptor are used to determine the presence and efficiency of energy transfer. The classical equations used to measure energy transfer on ensembles of fluorophores are modified for single-molecule measurements. In contrast to ensemble measurements, dynamic events on a molecular scale are observable in single pair FRET measurements because they are not canceled out by random averaging. Monitoring conformational changes, such as rotations and distance changes on a nanometer scale, within single biological macromolecules, may be possible with single pair FRET.

Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis.

Fluorescent dye-labeled DNA primers have been developed that exploit fluorescence energy transfer (ET) to optimize the absorption and emission properties of the label. These primers carry a fluorescein derivative at the 5' end as a common donor and other fluorescein and rhodamine derivatives attached to a modified thymidine residue within the primer sequence as acceptors. Adjustment of the donor-acceptor spacing through the placement of the modified thymidine in the primer sequence allowed generation of four primers, all having strong absorption at a common excitation wavelength (488 nm) and fluorescence emission maxima of 525, 555, 580, and 605 nm. The ET efficiency of these primers ranges from 65% to 97%, and they exhibit similar electrophoretic mobilities by gel electrophoresis. With argon-ion laser excitation, the fluorescence of the ET primers and of the DNA sequencing fragments generated with ET primers is 2- to 6-fold greater than that of the corresponding primers or fragments labeled with single dyes. The higher fluorescence intensity of the ET primers allows DNA sequencing with one-fourth of the DNA template typically required when using T7 DNA polymerase. With single-stranded M13mp18 DNA as the template, a typical sequencing reaction with ET primers on a commercial sequencer provided DNA sequences with 99.8% accuracy in the first 500 bases. ET primers should be generally useful in the development of other multiplex DNA sequencing and analysis methods.

Quantum Dot-Sensitized Solar Cells Based on Directly Adsorbed Zinc Copper Indium Sulfide Colloids

Heavy metal-based quantum dots (QDs) have demonstrated to behave as efficient sensitizers in QD-sensitized solar cells (QDSSCs), as attested by the countless works and encouraging efficiencies reported so far. However, their intrinsic toxicity has arisen as a major issue for the prospects of commercialization. Here, we examine the potential of environmentally friendly zinc copper indium sulfide (ZCIS) QDs for the fabrication of liquid-junction QDSSCs by means of photoelectrochemical measurements. A straightforward approach to directly adsorb ZCIS QDs on TiO2 from a colloidal dispersion is presented. Incident photon-to-current efficiency (IPCE) spectra of sensitized photoanodes show a marked dependence on the adsorption time, with longer times leading to poorer performances. Cyclic voltammograms point to a blockage of the channels of the mesoporous TiO2 film by the agglomeration of QDs as the main reason for the decrease in efficiency. Photoanodes were also submitted to the ZnS treatment. Its effects on electron recombination with the electrolyte are analyzed through electrochemical impedance spectroscopy and photopotential measurements. The corresponding results bring out the role of the ZnS coating as a barrier layer preventing electron leakage toward the electrolyte, as argued in other QD-sensitized systems. The beneficial effect of the ZnS coating is ultimately reflected on the power conversion efficiency of complete devices, reaching values of 2 %. In a more general vein, through these findings, we aim to call the attention to the potentiality of this quaternary alloy, virtually unexplored as a light harvester for sensitized devices.

Interplay Between Structure, Stoichiometry, and Electron Transfer Dynamics in SILAR-based Quantum Dot-Sensitized Oxides

We quantify the rate and efficiency of picosecond electron transfer (ET) from PbS nanocrystals, grown by successive ionic layer adsorption and reaction (SILAR), into a mesoporous SnO2 support. Successive SILAR deposition steps allow for stoichiometry- and size-variation of the QDs, characterized using transmission electron microscopy. Whereas for sulfur-rich (p-type) QD surfaces substantial electron trapping at the QD surface occurs, for lead-rich (n-type) QD surfaces, the QD trapping channel is suppressed and the ET efficiency is boosted. The ET efficiency increase achieved by lead-rich QD surfaces is found to be QD-size dependent, increasing linearly with QD surface area. On the other hand, ET rates are found to be independent of both QD size and surface stoichiometry, suggesting that the donor–acceptor energetics (constituting the driving force for ET) are fixed due to Fermi level pinning at the QD/oxide interface. Implications of our results for QD-sensitized solar cell design are discussed.

Modulation of Translation Efficiency in S. cerevisiae by Codon Pairs and mRNA Structure

Thesis (Ph.D.)--University of Washington, 2016-06

Enhanced spin injection efficiency in ferromagnet/semiconductor tunnel junctions

Within the ballistic transport picture, we have investigated the spin-polarized transport properties of a ferromagnetic metal/two-dimensional semiconductor (FM/SM) hybrid junction and an FM/FM/SM structure using quantum tunnelling theory. Our calculations indicate explicitly that the low spin injection efficiency (SIE) from an FM into an SM, compared with a ferromagnet/normal metal junction, originates from the mismatch of electron densities in the FM and SM. To enhance the SIE from an FM into an SM, we introduce another FM film between them to form FM/FM/SM double tunnel junctions, in which the quantum interference effect will lead to the current polarization exhibiting periodically oscillating behaviour, with a variation according to the thickness of the middle FM film and/or its exchange energy strength. Our results show that, for some suitable values of these parameters, the SIE can reach a very high level, which can also be affected by the electron density in the SM electrode.

Quantum interference effects in a cavity QED system

We consider the effect of quantum interference on population distribution and photon statistics of a cavity field interacting with dressed states of a strongly driven three-level atom. We analyse three coupling configurations of the cavity field to the driven atom, with the cavity frequency tuned to the outer Rabi sideband, the inner Rabi sideband and the central frequency of the 'singly dressed' three-level atom. The quantum doubly dressed states for each configuration are identified and the population distribution and photon statistics are interpreted in terms of transitions among these dressed states and their populations. We find that the population distribution depends strongly on quantum interference and the cavity damping. For the cavity field tuned to the outer or inner Rabi sidebands the cavity damping induces transitions between the dressed states which are forbidden for the ordinary spontaneous emission. Moreover, we find that in the case of the cavity field coupled to the inner Rabi sideband the population distribution is almost Poissonian with a large average number of photons that can be controlled by quantum interference. This system can be considered as a one-atom dressed-state laser with controlled intensity.

Iterative quantum computations of HO2 bound states and resonances for J=4 and 5

Bound and resonance states of HO2 have been calculated by both the complex Lanczos homogeneous filter diagonalisation (LHFD) method(1,2) and the real Chebyshev filter diagonalisation method(3,4) for non-zero total angular momentum J = 4 and 5. For bound states, the agreement between the two methods is quite satisfactory; for resonances while the energies are in good agreement, the widths are only in general agreement. The relative performances of the two iterative FD methods have also been discussed in terms of efficiency as well as convergence behaviour for such a computationally challenging problem. A helicity quantum number Ohm assignment (within the helicity conserving approximation) is performed and the results indicate that Coriolis coupling becomes more important as J increases and the helicity conserving approximation is not a good one for the HO2 resonance states.

Fluorescence in situ hybridization analysis of nitrifiers in piggery wastewater treatment reactors

Fluorescence in situ hybridization (FISH) was performed to analyze the nitrifying microbial communities in an activated sludge reactor (ASR) and a fixed biofilm reactor (FBR) for piggery wastewater treatment. Heterotrophic oxidation and nitrification were occurring simultaneously in the ASR and the COD and nitrification efficiencies depend on the loads. In the FBR nitrification efficiency also depends on ammonium load to the reactor and nitrite was accumulated when free ammonia concentration was higher than 0.2 mg NH3-N/L. FISH analysis showed that ammonia-oxidizing bacteria (NSO1225) and denitrifying bacteria (RRP1088) were less abundant than other bacteria (EUB338) in ASR. Further analysis on nitrifying bacteria in the FBR showed that Nitrosomonas species (NSM156) and Nitrospira species (NSR1156) were the dominant ammonia-oxidizing and nitrite-oxidizing bacteria, respectively, in the piggery wastewater nitrification system.

Absorption and fluorescence spectroscopy of rhodamine 6G in titanium dioxide nanocomposites

A comparison has been made between the spectroscopic properties of the laser dye rhodamine 6G (R6G) in mesostructured titanium dioxide (TiO2) and in ethanol. Steady-state excitation and emission techniques have been used to probe the dye-matrix interactions. We show that the TiO2-nanocomposite studied is a good host for R6G, as it allows high dye concentrations, while keeping dye molecules isolated, and preventing aggregation. Our findings have important implications in the context of solid state dye-lasers and microphotonic device applications. (C) 2003 Elsevier B.V. All rights reserved.

Simulating quantum interference in a three-level system with perpendicular transition dipole moments

We consider a three-level V-type atomic system with the ground state coupled by a laser field to only one of the excited states, and with the two excited states coupled together by a dc field. Although the dipole moments of the two dipole-allowed transitions are assumed perpendicular, we demonstrate that this system emulates to a large degree a three-level system with parallel dipole moments-the latter being a system that exhibits quantum interference and displays a number of interesting features. As examples, we show that the system can produce extremely large values for the intensity-intensity correlation function, and that its resonance fluorescence spectrum can display ultranarrow lines. The dressed states for this system are identified, and the spectral features are interpreted in terms of transitions among these dressed states. We also show that this system is capable of exhibiting considerable squeezing.

Testing the 'photoinhibition' model of coral bleaching using chemical inhibitors

Explants of the hard coral Seriatopora hystrix were exposed to sublethal concentrations of the herbicide diuron DCMU (N'-(3,4-dichlorophenyl,-N,N-dimethylurea)) and the heavy metal copper. Pulse amplitude modulated (PAM) chlorophyll fluorescence techniques were used to assess the effects on the photosynthetic efficiency of the algal symbionts in the tissue (in Symbio), and chlorophyll fluorescence and counts of symbiotic algae (normalised to surface area) were used to assess the extent of coral bleaching. At 30 mug DCMU l(-1), there was a reduction in both the maximum effective quantum yield (DeltaF/F-m') and maximum potential quantum yield (F-v/F-m) of the algal symbionts in symbio. Corals subsequently lost their algal symbionts and discoloured (bleached), especially on their upper sunlight-exposed surfaces. At the same DCMU concentration but under low light (5% of growth irradiance), there was a marked reduction in DeltaF/F-m' but only a slight reduction in F-v/F-m and slight loss of algae. Loss of algal symbionts was also noted after a 7 d exposure to concentrations as low as 10 mug DCMU l(-1) under normal growth irradiance, and after 14 d exposure to 10 mug DCMU l(-1) under reduced irradiance. Collectively the results indicate that DCMU-induced bleaching is caused by a light-dependent photoinactivation of algal symbionts, and that bleaching occurs when F-v/F-n, (measured 2 h after sunset) is reduced to a value of less than or equal to 0.6. Elevated copper concentrations (60 mug Cu l(-1) for 10 h) also induced a rapid bleaching in S. hystrix but without affecting the quantum yield of the algae in symbio. Tests with isolated algae indicated that substantially higher concentrations (300 mug Cu l(-1) for 8 h) were needed to significantly reduce the quantum yield. Thus, copper-induced bleaching occurs without affecting the algal photosynthesis and may be related to effects on the host (animal). It is argued that warm-water bleaching of corals resembles both types of chemically induced bleaching, suggesting the need for an integrated model of coral bleaching involving the effect of temperature on both host (coral) and algal symbionts.

Ion trap transducers for quantum electromechanical oscillators

An enduring challenge for contemporary physics is to experimentally observe and control quantum behavior in macroscopic systems. We show that a single trapped atomic ion could be used to probe the quantum nature of a mesoscopic mechanical oscillator precooled to 4 K, and furthermore, to cool the oscillator with high efficiency to its quantum ground state. The proposed experiment could be performed using currently available technology.

Effects of the herbicide diuron on the early life history stages of coral

The effects of the herbicide diuron on the early life history stages of broadcast spawning and brooding corals were examined in laboratory experiments. Fertilisation of Acropora millepora and Montipora aequituberculata oocytes were not inhibited at diuron concentrations of up to 1000 mu gl(-1). Metamorphosis of symbiont-free A. millepora larvae was only significantly inhibited at 300 mu gl(-1) diuron. Pocillopora damicornis larvae, which contain symbiotic dinoflagellates, were able to undergo metamorphosis after 24h exposure to diuron at 1000 mu gl(-1). Two-week old P. damicornis recruits on the other hand were as susceptible to diuron as adult colonies, with expulsion of symbiotic dinoflagellates (bleaching) evident at 10 mu gl(-1) diuron after 96 h exposure. Reversible metamorphosis was observed at high diuron concentrations, with fully bleached polyps escaping from their skeletons. Pulse amplitude modulation (PAM) chlorophyll fluorescence techniques demonstrated a reduction in photosynthetic efficiency (Delta F/F'(m)) in illuminated P. dami- cornis recruits after a 2h exposure to 1 mu gl(-1) diuron. The dark-adapted quantum yields (F-v/F-m also declined, indicating chronic photoinhibition and damage to photosystem H. Crown Copyright (c) 2004 Published by Elsevier Ltd. All rights reserved.

Effect of seasonal variation and storage temperature on leaf chlorophyll fluorescence and vase life of cut roses

Low temperature injury (LTI) of roses (Rosa hybrida L.) is difficult to assess by visual observation. Relative chlorophyll fluorescence (CF; F-v/F-m) is a non-invasive technique that provides an index of stress effects on photosystem 11 (PS 11) activity. This instrumental technique allows determination of the photosynthetic efficiency of plant tissues containing chloroplasts, such as rose leaves. In the present study, pre- and Post-Storage measurements of F-v/F-m were carried out to assess LTI in 'First Red' and 'Akito' roses harvested year round. Relationships between the pre-harvest environment conditions of temperature, relative humidity and photon flux density (PFD), F-v/F-m, and, vase life duration after storage are reported. After harvest, roses were stored at 1, 5 and 10 degrees C for 10 days. Non-stored roses were the control treatment. F-v/F-m ratios were reduced following storage, suggesting LTI of roses. However, reductions in F-v/F-m were not closely correlated with reduced vase life duration and were seasonally dependent. Only during winter experiments was F-v/F-m of roses stored at 1 degrees C significantly (P <= 0.001) lower compared to F-v/F-m of non-stored control roses and roses stored at 5 and 10 degrees C. Thus, the fall of F-v/F-m was due to an interaction of growing season and storage at 1 degrees C. Vase lives of roses grown during winter were significantly (P <= 0.001) shorter compared to roses grown during summer. Length of vase life was intermediate for roses grown during autumn and spring. Because of the lack of correlation between F-v/F-m and post-storage vase life it is concluded that the CF parameter F-v/F-m is nota practical index for assessing LTI in cold-stored roses. Higher PFD and temperature in summer were positively and significantly correlated with maintenance of post-storage FvIF ratios and longer vase life. It is suggested that shorter vase lives and lower post-storage F-v/F-m values after storage at 1 degrees C are consequences of reduced photosynthesis and smaller carbohydrate pools in winter-harvested roses. (c) 2004 Elsevier B.V All rights reserved.