Theory of light quenching: effects of fluorescence polarization, intensity, and anisotropy decays.

Experimental studies have recently demonstrated that fluorescence emission can be quenched by laser light pulses from modern high repetition rate lasers, a phenomenon we call "light quenching." We now describe the theory of light quenching and some of its effects on the steady-state and time-resolved intensity and anisotropy decays of fluorophores. Light quenching can decrease or increase the steady-state or time-zero anisotropy. Remarkably, the light quenching can break the usual z axis symmetry of the excited-state population, and the emission polarization can range from -1 to +1 under selected conditions. The measured anisotropy (or polarization) depends upon whether the observation axis is parallel or perpendicular to the propagation direction of the light quenching beam. The effects of light quenching are different for a single pulse, which results in both excitation and quenching, as compared with a time-delayed quenching pulse. Time-delayed light quenching pulses can result in step-like changes in the time-dependent intensity or anisotropy and are predicted to cause oscillations in the frequency-domain intensity and anisotropy decays. The increasing availability of pulsed laser sources offers the opportunity for a new class of two-pulse or multiple-pulse experiments where the sample is prepared by an excitation pulse, the excited state population is modified by the quenching pulse(s), followed by time- or frequency-domain measurements of the resulting emission.     

Photoisomerization and photoionization of the photoactive yellow protein chromophore in solution

Dispersed pump-dump-probe spectroscopy has the ability to characterize and identify the underlying ultrafast dynamical processes in complicated chemical and biological systems. This technique builds on traditional pump-probe techniques by exploring both ground- and excited-state dynamics and characterizing the connectivity between constituent transient states. We have used the dispersed pump-dump-probe technique to investigate the ground-state dynamics and competing excited-state processes in the excitation-induced ultrafast dynamics of thiomethyl p-coumaric acid, a model chromophore for the photoreceptor photoactive yellow protein. Our results demonstrate the parallel formation of two relaxation pathways (with multiple transient states) that jointly lead to two different types of photochemistry: cis-trans isomerization and detachment of a hydrated electron. The relative transition rates and quantum yields of both pathways have been determined. We find that the relaxation of the photoexcited chromophores involves multiple, transient ground-state intermediates and the chromophore in solution does not generate persistent photoisomerized products, but instead undergoes photoionization resulting in the generation of detached electrons and radicals. These results are of great value in interpreting the more complex dynamical changes in the optical properties of the photoactive yellow protein.     

Femtosecond pump-probe spectroscopy of bacteriochlorophyll a monomers in solution.

One- and two-color absorption difference profiles were obtained for BChl a in 1-propanol with approximately 50-fs resolution, using a self-mode-locked Ti:sapphire laser system. Time evolution in the BChl a absorption difference spectrum produces nonexponential photobleaching/stimulated emission (PB/SE) decay kinetics in 800-nm one-color experiments. Nonexponential PB/SE rise behavior occurs for some combinations of pump and probe wavelengths in two-color experiments. Optimized parameters from triexponential fits to the absorption difference profiles depend markedly on the fitting time window; they typically include a minor component with lifetime in the hundreds of fs. Much of the latter component is due to vibrational relaxation and/or intramolecular vibrational redistribution, rather than solvent dielectric relaxation. Measurements of the pump-probe anisotropy indicate that the electronic transition moment for the broad Qy excited state absorption band that overlaps the Qy steady-state absorption spectrum makes an angle of at most 20 degrees from that of the ground-->Qy state transition. No coherent oscillations are observed at early times. Our results bear directly on the interpretation of fs pump-probe experiments on BChl a-containing pigment-protein complexes.     

Two-photon absorption of bacteriorhodopsin: formation of a red-shifted thermally stable photoproduct F620

By means of high-intensity 532 nm laser pulses, a photochemical conversion of the initial B(570) state of bacteriorhodopsin (BR) to a stable photoproduct absorbing maximally at approximately 620 nm in BR suspensions and at approximately 610 nm in BR films is induced. This state, which we named F(620), is photochemically further converted to a group of three products with maximal absorptions in the wavelength range from 340 nm to 380 nm, which show identical spectral properties to the so-called P(360) state reported in the literature. The photoconversion from B(570) to F(620) is most likely a resonant two-photon absorption induced step. The formation of F(620) and P(360) leads to a distinguished photo-induced permanent optical anisotropy in BR films. The spectral dependence of the photo-induced anisotropy and the anisotropy orientations at the educt (B(570)) and product (F(620)) wavelengths are strong indicators that F(620) is formed in a direct photochemical step from B(570). The chemical nature of the P(360) products probably is that of a retro-retinal containing BR, but the structural characteristics of the F(620) state are still unclear. The photo-induced permanent anisotropy induced by short laser pulses in BR films helps to better understand the photochemical pathways related to this transition, and it is interesting in view of potential applications as this feature is the molecular basis for permanent optical data storage using BR films.     

Miniaturization capable, very sensitive polarimeter as detector of an implantable glucose probe. I. Optical amplification of the measuring value]

From a clinical point of view, an implantable telemetric probe for monitoring the blood glucose profile is highly desirable. It should be capable of monitoring the blood glucose level continuously or at regular brief intervals, if necessary requirement-controlled. Apart from blood, measurement can also be made in intercellular tissue fluid, for example, in subcutaneous connective and fatty tissue, because this fluid accurately reflects blood glucose levels after only a brief, but negligible, time lag. Since the functional lifespan of an implantable probe is of decisive importance, only physical sensors, but not bio-sensors can be considered. We are in the process of developing a very sensitive miniaturised detector based on polarimetry, capable of determining the measuring parameter--the spatial orientation of the in-plane vibration of a polarised light beam--with extreme accuracy. This is a very important point, since the physiological and pathological glucose levels modify the in-plane vibration by only a very tiny angle of rotation. The high level of accuracy is achieved by various specific optical amplification mechanisms, and amplification of the electric signal. Two purely optical amplification methods are described here. Simple linear elongation of the optical path of a laser beam within the sample, resulting in a proportional amplification of the measuring signal, is obviously strictly limited in an implantable probe. We therefore developed a technique that preserves the polarisation state of the light beam during reflection. This technique makes possible multiple passage of the light beam through the fluid being sensed, thus elongating the optical path by "folding" the light beam without the need to enlarge the measuring cuvette. In a second possibility, enlargement of the rotation angle can be achieved by reflecting the light beam from a suitable surface, when the orthogonal components of the polarised light beam are reflected to different extents.     

Mobility measurement by analysis of fluorescence photobleaching recovery kinetics.

Fluorescence photobleaching recovery (FPR) denotes a method for measuring two-dimensional lateral mobility of fluorescent particles, for example, the motion of fluorescently labeled molecules in approximately 10 mum2 regions of a single cell surface. A small spot on the fluorescent surface is photobleached by a brief exposure to an intense focused laser beam, and the subsequent recovery of the fluorescence is monitored by the same, but attenuated, laser beam. Recovery occurs by replenishment of intact fluorophore in the bleached spot by lateral transport from the surrounding surface. We present the theoretical basis and some practical guidelines for simple, rigorous analysis of FPR experiments. Information obtainable from FPR experiments includes: (a) identification of transport process type, i.e. the admixture of random diffusion and uniform directed flow; (b) determination of the absolute mobility coefficient, i.e. the diffusion constant and/or flow velocity; and (c) the fraction of total fluorophore which is mobile. To illustrate the experimental method and to verify the theory for diffusion, we describe some model experiments on aqueous solutions of rhodamine 6G.     

Vacuum electron acceleration by a tightly focused,radially polarized,relativistically strong laser pulse

A test particle approach is used to solve the problem of direct electron acceleration by a short, intense, radially polarized laser pulse the focal spot diameter of which can be on the order of the laser wavelength. The fields of a tightly focused laser beam are described in terms of the Stratton-Chu integrals, with which to investigate electron acceleration when the paraxial approximation is inapplicable to laser fields. The dynamics of electron motion in a radially polarized, relativistically strong laser field is analyzed depending on the initial position of an electron in the focal region of the laser beam. The properties of the generated jets of accelerated electrons are investigated depending on the tightness of laser pulse focusing. Possible advantages of using radially polarized laser pulses for charged particle acceleration, as opposed to the use of linearly polarized ones, are discussed.     

Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods

Background

Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human splicing branchpoints, but many branchpoints are still unknown. In order to guide wet experiments, we develop computational methods to predict human splicing branchpoints.

Results

Considering the fact that an intron may have multiple branchpoints, we transform the branchpoint prediction as the multi-label learning problem, and attempt to predict branchpoint sites from intron sequences. First, we investigate a variety of intron sequence-derived features, such as sparse profile, dinucleotide profile, position weight matrix profile, Markov motif profile and polypyrimidine tract profile. Second, we consider several multi-label learning methods: partial least squares regression, canonical correlation analysis and regularized canonical correlation analysis, and use them as the basic classification engines. Third, we propose two ensemble learning schemes which integrate different features and different classifiers to build ensemble learning systems for the branchpoint prediction. One is the genetic algorithm-based weighted average ensemble method; the other is the logistic regression-based ensemble method.

Conclusions

In the computational experiments, two ensemble learning methods outperform benchmark branchpoint prediction methods, and can produce high-accuracy results on the benchmark dataset.

     

Femtosecond energy transfer and spectral equilibration in bacteriochlorophyll a--protein antenna trimers from the green bacterium Chlorobium tepidum.

Femtosecond energy transfer processes in a bacteriochlorophyll a-protein antenna complex from the green sulfur bacterium Chlorobium tepidum have been studied by one-color, two-color, and broadband absorption difference spectroscopy. Much of the spectral excitation equilibration in this antenna occurs with 350 to 450 fs kinetics. The anisotropy decay functions r(t) exhibit two major lifetime components, 100 to 130 fs and 1.7 to 2.0 ps. The short component lifetimes may represent single-step energy transfer kinetics in this antenna; the long component is similar to the anisotropy decay observed in earlier picosecond pump-probe experiments.     

Optimization of the Field Enhancement and Spectral Bandwidth of Single and Coupled Bimetal Core–Shell Nanoparticles for Few-Cycle Laser Applications

We have theoretically studied and optimized the field enhancement and temporal response of single and coupled bimetal Ag/Au core–shell nanoparticles (NPs) with a diameter of 160 nm and compared the results to pure Ag and Au NPs. Very high-field enhancements with an amplitude reaching 100 (with respect to the laser field centered at 800 nm) are found at the center of a 2-nm gap between Ag/Au core–shell dimers. We have explored the excitation of the bimetal core–shell particles by Fourier transform-limited few-cycle optical pulses and identified conditions for an ultrafast plasmonic decay on the order of the excitation pulse duration. The high-field enhancement and ultrafast decay makes bimetal core–shell particles interesting candidates for applications such as the generation of ultrashort extreme ultraviolet radiation pulses via nanoplasmonic field enhancement. Moreover, in first experimental studies, we synthesized small bimetal Ag/Au core–shell NPs and compared their optical response with pure Au and Ag NPs and numerical results.     

Low-temperature energy transfer in FMO trimers from the green photosynthetic bacterium Chlorobium tepidum

The pump-probe kinetics of the slowest spectral equilibrations between inequivalent BChl a Q_y states in FMO trimers from Chlorobium tepidum are decelerated by nearly two orders of magnitude when the temperature is lowered from 300 K to 19 K. The pump-probe anisotropy decays are also markedly slower at 19 K than at 300 K. Singlet-singlet annihilation in FMO trimers is negligible at the laser powers used here. However, reduced temperatures greatly accentuate the probability of singlet-triplet annihilation, due to accumulation of metastable BChl a states under high laser repetition rates.Abbreviations BChl bacteriochlorophyll - FMO Fenna-Matthews-Olson - fwhm full width at half maximum - PB photobleaching - SE stimulated emission     

Time-resolved methods in biophysics. 4. Broadband pump-probe spectroscopy system with sub-20 fs temporal resolution for the study of energy transfer processes in photosynthesis.

In this paper we discuss how to push the temporal resolution limits of transient absorption spectroscopy in order to detect very fast processes (energy relaxation, energy or charge transfer, vibrational coherence) taking place in molecules of biological relevance. After reviewing the main principles of femtosecond pump-probe spectroscopy, we describe an experimental setup based on two synchronized non-collinear optical parametric amplifiers (NOPAs). Each NOPA can be independently configured to generate ultra-broadband sub-10 fs visible pulses, tunable 10-15 fs visible pulses, tunable 15-40 fs near-infrared pulses (900-1500 nm). This system enables to perform pump-probe experiments over nearly two octaves of spectrum with sub-20 fs temporal resolution. We then present an application example highlighting the capability of this instrument to track excited state dynamics in biomolecules on the sub-100 fs timescale: the study of carotenoid-bacteriochlorophyll energy transfer processes in peripheral light-harvesting complexes (LH2) from purple bacteria. We show that, by comparing excited-state dynamics of the carotenoids in organic solvents and inside the LH2 complexes, it is possible to visualize in the time domain the primary events in photosynthesis.     

Effects of Carrier Confinement and Intervalley Scattering on Photoexcited Electron Plasma in Silicon

The ultrafast reflectivity of silicon, excited and probed with femtosecond laser pulses, is studied for different wavelengths and energy densities. The confinement of carriers in a thin surface layer delimited by a nanoscale Si-layered system buried in a Si heavily-doped wafer reduces the critical density of carriers necessary to create the electron plasma by a factor of ten. We performed two types of reflectivity measurements, using either a single beam or two beams. The plasma strongly depends on the photon energy density because of the intervalley scattering of the electrons revealed by two different mechanisms assisted by the electron–phonon interaction. One mechanism leads to a negative differential reflectivity that can be attributed to an induced absorption in X valleys. The other mechanism occurs, when the carrier population is thermalizing and gives rise to a positive differential reflectivity corresponding to Pauli-blocked intervalley gamma to X scattering. These results are important for improving the efficiency of Si light-to-electricity converters, in which there is a possibility of multiplying carriers by nanostructurization of Si.     

Improved quantification of collagen anisotropy with polarization‐resolved second harmonic generation microscopy

Imaging tissue samples by polarization‐resolved second harmonic generation microscopy provides both qualitative and quantitative insights into collagen organization in a label‐free manner. Polarization‐resolved second harmonic generation microscopy goes beyond simple intensity‐based imaging by adding the laser beam polarization component and applying different quantitative metrics such as the anisotropy factor. It thus provides valuable information on collagen arrangement not available with intensity measurements alone. Current established approaches are limited to calculating the anisotropy factor for only a particular laser beam polarization and no general guidelines on how to select the best laser beam polarization have yet been defined. Here, we introduce a novel methodology for selecting the optimal laser beam polarization for characterizing tissues using the anisotropy in the purpose of identifying cancer signatures. We show that the anisotropy factor exhibits a similar laser beam polarization dependence to the second harmonic intensity and we combine it with the collagen orientation index computed by Fast Fourier Transform analysis of the recorded images to establish a framework for choosing the laser beam polarization that is optimal for an accurate interpretation of polarization‐resolved second harmonic generation microscopy images and anisotropy maps, and hence a better differentiation between healthy and dysplastic areas.

SHG image of skin tissue (a) and a selected area of interest for which we compute the SHG intensity (b) and anisotropy factor (c) dependence on the laser beam polarization and also the FFT spectrum (d) to evaluate the collagen orientation index.     

One- and two-photon-induced fluorescence from recombinant green fluorescent protein

The fluorescence spectral properties of recombinant green fluorescent protein (rGFP) were examined with one- and two-photon excitations using femtosecond pulses from a Ti:sapphire laser. Intensity-dependent properties of the two-photon-induced fluorescence from rGFP excited by an 800-nm, 100-fs laser beam were reported, and the two-photon excitation cross section of rGFP was measured at 800 nm as about 160 x 10(-50) cm(4)s/photon. The possible excited-state proton transfer between two electronic states at about 400 nm in protonated (RH) species and 478 nm in deprotonated (R(-)) species in rGFP was confirmed by fluorescence and fluorescence excitation anisotropy spectra. A subelectronic state (or vibronic progression) at about 420 nm in RH species was identified, which was relatively stable and not involved in the excited state proton transfer in rGFP upon irradiation.     

Short-pulse pump-and-probe technique for airborne laser assessment of Photosystem II photochemical characteristics

The development of a technique for laser measurement of fPhotosystem II (PS II) photochemical characteristics of phytoplankton and terrestrial vegetation from an airborne platform is described. Results of theoretical analysis and experimental study of pump-and-probe measurement of the PS II functional absorption cross-section and photochemical quantum yield are presented. The use of 10 ns probe pulses of PS II sub-saturating intensity provides a significant, up to 150-fold, increase in the fluorescence signal compared to conventional `weak-probe' protocol. Little effect on the fluorescence yield from the probe-induced closure of PS II reaction centers is expected over the short pulse duration, and thus a relatively intense probe pulse can be used. On the other hand, a correction must be made for the probe-induced carotenoid triplet quenching and singlet-singlet annihilation. A Stern-Volmer model developed for this correction assumes a linear dependence of the quenching rate on the laser pulse fluence, which was experimentally validated. The PS II saturating pump pulse fluence (532 nm excitation) was found to be 10 and 40 μmol quanta m⁻² for phytoplankton samples and leaves of higher plants, respectively. Thirty μs was determined as the optimal delay in the pump-probe pair. Our results indicate that the short-pulse pump-and-probe measurement of PS II photochemical characteristics can be implemented from an airborne platform using existing laser and LIDAR technologies. This revised version was published online in June 2006 with corrections to the Cover Date.     

Enhancing the Strength of an Optical Trap by Truncation

Optical traps (tweezers) are beginning to be used with increasing efficacy in diverse studies in the biological and biomedical sciences. We report here results of a systematic study aimed at enhancing the efficiency with which dielectric (transparent) materials can be optically trapped. Specifically, we investigate how truncation of the incident laser beam affects the strength of an optical trap in the presence of a circular aperture. Apertures of various sizes have been used by us to alter the beam radius, thereby changing the effective numerical aperture and intensity profile. We observe significant enhancement of the radial and axial trap stiffness when an aperture is used to truncate the beam compared to when no aperture was used, keeping incident laser power constant. Enhancement in trap stiffness persists even when the beam intensity profile is modulated. The possibility of applying truncation to multiple traps is explored; to this end a wire mesh is utilized to produce multiple trapping that also alters the effective numerical aperture. The use of a mesh leads to reduction in trap stiffness compared to the case when no wire mesh is used. Our findings lead to a simple-to-implement and inexpensive method of significantly enhancing optical trapping efficiency under a wide range of circumstances.     

Fluorescence lifetime imaging by asynchronous pump-probe microscopy.

We report the development of a scanning lifetime fluorescence microscope using the asynchronous, pump-probe (stimulated emission) approach. There are two significant advantages of this technique. First, the cross-correlation signal produced by overlapping the pump and probe lasers results in i) an axial sectioning effect similar to that in confocal and two-photon excitation microscopy, and ii) improved spatial resolution compared to conventional one-photon fluorescence microscopy. Second, the low-frequency, cross-correlation signal generated allows lifetime-resolved imaging without using fast photodetectors. The data presented here include 1) determination of laser sources' threshold powers for linearity in the pump-probe signal; 2) characterization of the pump-probe intensity profile using 0.28 microns fluorescent latex spheres; 3) high frequency (up to 6.7 GHz) lifetime measurement of rhodamine B in water; and 4) lifetime-resolved images of fluorescent latex spheres, human erythrocytes and a mouse fibroblast cell stained by rhodamine DHPE, and a mouse fibroblast labeled with ethidium bromide and rhodamine DHPE.