Molecular organization in protein-lipid film on the water surface studied by x-ray standing wave measurements under total external reflection

The x-ray standing wave method has been applied to study self-assembling processes in a protein-lipid film formed by injecting the protein-lipid mixture of alkaline phosphatase and phosphatidylinositol under the phospholipid monolayer preliminarily deposited on the water subphase by Langmuir method. X-ray standing wave measurements allowed to determine the composition of the protein-lipid film and to locate ions position in the direction normal to the film surface. The presence of trace Ni contamination incorporated in the protein-lipid film from the water subphase has been established. Numerical analysis of the X-ray standing wave fluorescence data revealed that after injection under the phospholipid monolayer, the protein-lipid mixture separated in a self-assembled manner to layered structure, molecules of alkaline phosphatase arranged themselves into a pure protein layer containing no phospholipid molecules.     

Arrangement of trace metal contaminations in thin films of liquid crystals studied by X-ray standing wave technique

X-ray standing wave method has been applied to investigate the molecular organization in Langmuir–Blodgett films of liquid-crystalline lanthanide complex deposited on silicon substrates. The X-ray standing waves measurements were carried out at BESSY II on the beamline KMC-2. Energy spectra of characteristic fluorescence emitted from the samples have been recorded at each point in the X-ray reflectivity curve as the incident angle was scanned through the total external reflection region. The integrated intensity under selected peaks was analyzed as a function of the incident angle. Incorporation of metal ions (Fe, Zn, Cu, Ca) to the Langmuir monolayer from the triply distilled water subphase has been established. Owing to the element selectivity of X-ray standing wave technique the arrangement of several types of metal ions inside the Langmuir–Blodgett films was studied individually. The experimental data revealed that the shape of the fluorescence curves for the contamination metal ions is distinctly different indicating considerable differences in the lateral distribution of these ions in the film. These results may be attributed to the phase separation in Langmuir monolayer of liquid-crystalline lanthanide complex due to the incorporation of metal ions from the water subphase.     

Acoustic resonances in microfluidic chips: full-image micro-PIV experiments and numerical simulations

We show that full-image micro-PIV analysis in combination with images of transient particle motion is a powerful tool for experimental studies of acoustic radiation forces and acoustic streaming in microfluidic chambers under piezo-actuation in the MHz range. The measured steady-state motion of both large 5 microm and small 1 microm particles can be understood in terms of the acoustic eigenmodes or standing ultra-sound waves in the given experimental microsystems. This interpretation is supported by numerical solutions of the corresponding acoustic wave equation.     

Depth profile characterization of ultra shallow junction implants

A need for analysis techniques, complementary to secondary ion mass spectrometry (SIMS), for depth profiling dopants in silicon for ultra shallow junction (USJ) applications in CMOS technologies has recently emerged following the difficulties SIMS is facing there. Grazing incidence X-ray fluorescence (GIXRF) analysis in the soft X-ray range is a high-potential tool for this purpose. It provides excellent conditions for the excitation of the B-K and the As-L _iii,ii shells. The X-ray standing wave (XSW) field associated with GIXRF on flat samples is used here as a tunable sensor to obtain information about the implantation profile because the in-depth changes of the XSW intensity are dependent on the angle of incidence. This technique is very sensitive to near-surface layers and is therefore well suited for the analysis of USJ distributions. Si wafers implanted with either arsenic or boron at different fluences and implantation energies were used to compare SIMS with synchrotron radiation-induced GIXRF analysis. GIXRF measurements were carried out at the laboratory of the Physikalisch-Technische Bundesanstalt (PTB) at the electron storage ring BESSY II using monochromatized undulator radiation of well-known radiant power and spectral purity. The use of an absolutely calibrated energy-dispersive detector for the acquisition of the B-Kα and As-Lα fluorescence radiation enabled the absolute determination of the total retained dose. The concentration profile was obtained by ab initio calculation and comparison with the angular measurements of the X-ray fluorescence.     

Visualization of the microtubules of glutaraldehyde-fixed cells by reflection-enhanced backscatter confocal microscopy.

Performing reflection-mode (backscatter-mode) confocal microscopy on cells growing on reflective substrates gives images that have improved contrast and are more easily interpreted than standard reflection-mode confocal micrographs (Keith et al., 1998). However, a number of factors degrade the quality of images taken with the highest-resolution microscope objectives in this technique. We here describe modifications to reflection-enhanced backscatter confocal microscopy that (partially) overcome these factors. With these modifications of the technique, it is possible to visualize structures the size-and refractility-of individual microtubules in intact cells. Additionally, we demonstrate that this technique, in common with fluorescence techniques such as standing wave widefield fluorescence microscopy and 4-Pi confocal microscopy, offers improved resolution in the Z-direction.     

Hard X-ray micro-spectroscopy at Berliner Elektronenspeicherring für Synchrotronstrahlung II

The capabilities of the X-ray beamlines at Berliner Elektronenspeicherring für Synchrotronstrahlung II (BESSY II) for hard X-ray measurements with micro- and nanometer spatial resolution are reviewed. The micro-X-ray fluorescence analysis (micro-XRF), micro-extended X-ray absorption fine structure (micro-EXAFS), micro-X-ray absorption near-edge structure (micro-XANES) as well as X-ray standing wave technique (XSW), X-ray beam induced current (XBIC) in combination with micro-XRF and micro-diffraction as powerful methods for organic and inorganic sample characterization with synchrotron radiation are discussed. Mono and polycapillary optical systems were used for fine X-ray focusing down to 1 µm spot size with monochromatic and white synchrotron radiation. Polycapillary based confocal detection was applied for depth-resolved micro-XRF analysis with a volume resolution down to 3.4 · 10^− 6 mm³. Standing wave excitation in waveguides was also applied to nano-EXAFS measurements with depth resolution on the order of 1 nm. Several examples of the methods and its applications in material research, biological investigations and metal-semiconductor interfaces analysis are given.     

Electric field standing wave effects in FT-IR transflection spectra of biological tissue sections: Simulated models of experimental variability

The so-called electric field standing wave effect (EFSW) has recently been demonstrated to significantly distort FT-IR spectra acquired in a transflection mode, both experimentally and in simulated models, bringing into question the appropriateness of the technique for sample characterization, particularly in the field of spectroscopy of biological materials. The predicted effects are most notable in the regime where the sample thickness is comparable to the source wavelength. In this work, the model is extended to sample thicknesses more representative of biological tissue sections and to include typical experimental factors which are demonstrated to reduce the predicted effects. These include integration over the range of incidence angles, varying degrees of coherence of the source and inhomogeneities in sample thickness. The latter was found to have the strongest effect on the spectral distortions and, with inhomogeneities as low as 10% of the sample thickness, the predicted distortions due to the standing wave effect are almost completely averaged out. As the majority of samples for biospectroscopy are prepared by cutting a cross section of tissue resulting in a high degree of thickness variation, this finding suggests that the standing wave effect should be a minor distortion in FT-IR spectroscopy of tissues. The study has important implications not only in optimization of protocols for future studies, but notably for the validity of the extensive studies which have been performed to date on tissue samples in the transflection geometry.     

Spatiotemporal chaos arising from standing waves in a reaction-diffusion system with cross-diffusion

We show that quasi-standing wave patterns appear in the two-variable Oregonator model of the Belousov-Zhabotinsky reaction when a cross-diffusion term is added, no wave instability is required in this case. These standing waves have a frequency that is half the frequency of bulk oscillations displayed in the absence of diffusive coupling. The standing wave patterns show a dependence on the systems size. Regular standing waves can be observed for small systems, when the system size is an integer multiple of half the wavelength. For intermediate sizes, irregular patterns are observed. For large sizes, the system shows an irregular state of spatiotemporal chaos, where standing waves drift, merge, and split, and also phase slips may occur.     

Determination of zirconium in zirconium-bearing sands and zirconium concentrates by a nondispersive x-ray fluorescence method

A nondispersive X-ray fluorescence; method for the rapid, nondestructive determination of zirconium in zirconium-bearing sands and zirconium concentrates is described. A ¹⁰⁹Cd source of primary radiation and compact geometry for measurements were used. The matrix effect from iron and titanium in sands was eliminated by measuring the fluorescent radiation of zirconium and the scattered primary radiation, and interpreting the data with nomograms. For concentrates, dilution with pure sand and measurement of the ratio of fluorescence to scattered radiation were used to reduce a matrix effect; a calibration curve was then satisfactory. Particle size effects were avoided by grinding to below 70 μ.     

Total reflection X-ray fluorescence study of organic nanostructures

X-ray scattering techniques based on total external fluorescence study and development of X-ray standing wave method are presented and used for characterization of organic nanostructure Langmuir–Blodgett films of fatty acid salts and phospholipids. Spectral selectivity of data obtained allows us to detect structure position of different ions in organic systems, to obtain information about interdiffusion at the interfaces, about ion permeation through organic bilayers, thus allowing us to develop models of biomembranes.     

Theoretical analysis and computer simulation of fluorescence lifetime measurements. I. Kinetic regimes and experimental time scales

The configuration-controlled regime and the diffusion-controlled regime of conformation-modulated fluorescence emission are systematically studied for Markovian and non-Markovian dynamics of the reaction coordinate. A path integral simulation is used to model fluorescence quenching processes on a semiflexible chain. First-order inhomogeneous cumulant expansion in the configuration-controlled regime defines a lower bound for the survival probability, while the Wilemski-Fixman approximation in the diffusion-controlled regime defines an upper bound. Inclusion of the experimental time window of the fluorescence measurement adds another dimension to the two kinetic regimes and provides a unified perspective for theoretical analysis and experimental investigation. We derive a rigorous generalization of the Wilemski-Fixman approximation [G. Wilemski and M. Fixman, J. Chem. Phys. 60, 866 (1974)] and recover the 1/D expansion of the average lifetime derived by Weiss [G. H. Weiss, J. Chem. Phys. 80, 2880 (1984)].     

Influence of the energy of primary radiation on the sensitivity of x-ray fluorescence analysis

Theoretical considerations and experimental data are presented concerning the influence of the energy of the primary radiation on the sensitivity of X-ray fluorescence analysis. An additional criterion in selecting the energy of the primary radiation based on the relative sensitivity of X-ray fluoresence analysis depends on the energy of the primary radiation and it becomes higher with the increase of this energy.     

Fluctuating Interfaces in Liquid Crystals

Summary: We review and compare recent work on the properties of fluctuating interfaces between isotropic and nematic liquid-crystalline phases. Molecular dynamics and Monte Carlo simulations have been carried out for systems of ellipsoids and hard rods with aspect ratio 15:1, and the fluctuation spectrum of interface positions (the capillary wave spectrum) has been analyzed. In addition, the capillary wave spectrum has been calculated analytically within the Landau-de Gennes theory. The theory predicts that the interfacial fluctuations can be described in terms of a wave vector dependent interfacial tension, which is anisotropic at small wavelengths (stiff director regime) and becomes isotropic at large wavelengths (flexible director regime). After determining the elastic constants in the nematic phase, theory and simulation can be compared quantitatively. We obtain good agreement for the stiff director regime. The crossover to the flexible director regime is expected at wavelengths of the order of several thousand particle diameters, which was not accessible to our simulations.     

Effect of energy dependence of primary beam divergence on the X-ray standing wave characterization of layered materials.

Incident primary beam divergence is a source of systematic error in X-ray standing wave (XSW) characterization of single and multilayer thin films. Primary beam divergence significantly alters the XSW profile of a layered material and can lead to large errors when used with higher excitation energies. The present study suggests that when one uses Mo-Kalpha excitation, the primary beam divergence should be in range of 0.005(0). On the other hand, in the case of Cu-Kalpha excitation, primary beam divergence can be relaxed up to 0.01(0).     

Quantitative determination of the single-molecule detection regime in fluorescence fluctuation microscopy by means of photon counting histogram analysis

Fluorescence fluctuation experiments are performed in single-molecule detection regime if the fluorescence of at most one molecule is registered at a time. Although the significance of such experiments for investigations of complex nonergodic systems like those met in the biosciences has been stressed out by many scientists, the quantitative and accurate determination of the single-molecule detection regime received rather little attention. In this work we present a method based on the photon counting histogram (PCH) analysis, which enables the determination of the average number N of molecules within the observation volume, for which only the fluorescence of individual molecules is detected at a time. Thus, the accurate design of fluorescence fluctuation experiments performed in single-molecule detection regime is possible. Demonstrative fluorescence fluctuation experiments based on two-photon excitation are performed on diluted solutions of coumarin 153, in order to verify the potential of the PCH analysis in experiments on the single-molecule detection level. If the mean number N of molecules within the excitation volume is larger than 0.048, the probability to simultaneously detect the fluorescence of two or more molecules is no longer negligible, i.e., no single-molecule detection regime. If the mean number N of molecules is lower than 0.0057, the detection limit of the method is reached, i.e., the fluorescence signal cannot be distinguished from the background. Consequently, the concentration of coumarin 153 characteristic for the single-molecule detection regime lies in the range 13-110 pmol/l for the given experimental conditions. We also investigate the influence of the molecular brightness, i.e., detected photons per fluorophore molecule and sampling time, on the single-molecule detection regime.     

Cavity ring-down spectroscopy measurement of single aerosol particle extinction. II. Extinction of light by an aerosol particle in an optical cavity excited by a cw laser

The authors present an analytical derivation of the scattered power from a spherical, homogeneous, nonabsorbing particle in a plane standing wave. The scattered power changes significantly with the position of the particle with respect to the peaks and nodes of the standing wave, even for particles whose diameters are many times the wavelength of the light. The analysis is applicable to continuous-wave cavity ring-down spectroscopy on aerosol particles, and the structure of the standing wave is expected to affect both the measured ring-down time and the shape of the ring-down trace. The dependence of the extinction on the phase of the standing wave at the location of the particle is captured in a parameter zeta which connects the current treatment to standard Mie scattering theory. Methods for calculating zeta are presented.     

Calculation of the contribution of scattering effects to X-ray fluorescence intensity for coating samples

Theoretical equations to calculate fluorescence intensity enhanced by scattering effects for coating samples were developed based on fundamental parameter models. The secondary enhancement by scattering radiation from the same layer or between layer and substrate and the primary fluorescence that was scattered into the direction of detector by atoms in layer and substrate were included in calculations. The contributions of different scattering effects to fluorescence intensity were calculated for a hypothetical Zn coating on infinite Fe substrate sample. The results show that the contributions of scattering effects to fluorescence intensity are related to the thickness of coating and are up to several percents of primary fluorescence intensity.     

Formation of the background component of the analytical signal in the long-wavelength region of X-ray fluorescence spectrum

Components of X-ray background in the long-wavelength spectral region of a crystal diffraction X-ray fluorescence spectrometer were calculated. The calculations took into account the bremsstrahlung radiation of free electrons, diffuse scattering and fluorescence of the crystal analyzer, and high-order reflections of the scattered radiation of the fluorescent sample by the crystal analyzer. The results of calculations were compared with the intensities of background samples measured in the region of the NaK _α fluorescence line on an SRM-25 wave X-ray spectrometer. The experimental background intensities (response function) well correlate with those found by the regression equation with calculated factors. The importance of particular processes in the formation of X-ray background was assessed.     

Jumping solitary waves in an autonomous reaction-diffusion system with subcritical wave instability

We describe a new type of solitary waves, which propagate in such a manner that the pulse periodically disappears from its original position and reemerges at a fixed distance. We find such jumping waves as solutions to a reaction-diffusion system with a subcritical short-wavelength instability. We demonstrate closely related solitary wave solutions in the quintic complex Ginzburg-Landau equation. We study the characteristics of and interactions between these solitary waves and the dynamics of related wave trains and standing waves.     

Chip integrated strategies for acoustic separation and manipulation of cells and particles

Acoustic standing wave technology combined with microtechnology opens up new areas for the development of advanced particle and cell separating microfluidic systems. This tutorial review outlines the fundamental work performed on continuous flow acoustic standing wave separation of particles in macro scale systems. The transition to the microchip format is further surveyed, where both fabrication and design issues are discussed. The acoustic technology offers attractive features, such as reasonable throughput and ability to separate particles in a size domain of about tenths of micrometers to tens of micrometers. Examples of different particle separation modes enabled in microfluidic chips, utilizing standing wave technology, are described along a discussion of several potential applications in life science research and in the medical clinic. Chip integrated acoustic standing wave separation technology is still in its infancy and it can be anticipated that new laboratory standards very well may emerge from the current research.