Chromophore structural changes in rhodopsin from nanoseconds to microseconds following pigment photolysis

Rhodopsin is a prototypical G protein-coupled receptor that is activated by photoisomerization of its 11-cis-retinal chromophore. Mutant forms of rhodopsin were prepared in which the carboxylic acid counterion was moved relative to the positively charged chromophore Schiff base. Nanosecond time-resolved laser photolysis measurements of wild-type recombinant rhodopsin and two mutant pigments then were used to determine reaction schemes and spectra of their early photolysis intermediates. These results, together with linear dichroism data, yielded detailed structural information concerning chromophore movements during the first microsecond after photolysis. These chromophore structural changes provide a basis for understanding the relative movement of rhodopsin’s transmembrane helices 3 and 6 required for activation of rhodopsin. Thus, early structural changes following isomerization of retinal are linked to the activation of this G protein-coupled receptor. Such rapid structural changes lie at the heart of the pharmacologically important signal transduction mechanisms in a large variety of receptors, which use extrinsic activators, but are impossible to study in receptors using diffusible agonist ligands.

Digital surface model, hillshade and orthophoto of the world's largest fossil oyster reef, links to GeoTIFFs

The world's largest fossil oyster reef, formed by the giant oyster Crassostrea gryphoides and located in Stetten (north of Vienna, Austria) is studied by Harzhauser et al., 2015, 2016; Djuricic et al., 2016. Digital documentation of the unique geological site is provided by terrestrial laser scanning (TLS) at the millimeter scale. Obtaining meaningful results is not merely a matter of data acquisition with a suitable device; it requires proper planning, data management, and postprocessing. Terrestrial laser scanning technology has a high potential for providing precise 3D mapping that serves as the basis for automatic object detection in different scenarios; however, it faces challenges in the presence of large amounts of data and the irregular geometry of an oyster reef. We provide a detailed description of the techniques and strategy used for data collection and processing in Djuricic et al., 2016. The use of laser scanning provided the ability to measure surface points of 46,840 (estimated) shells. They are up to 60-cm-long oyster specimens, and their surfaces are modeled with a high accuracy of 1 mm. In addition to laser scanning measurements, more than 300 photographs were captured, and an orthophoto mosaic was generated with a ground sampling distance (GSD) of 0.5 mm. This high-resolution 3D information and the photographic texture serve as the basis for ongoing and future geological and paleontological analyses. Moreover, they provide unprecedented documentation for conservation issues at a unique natural heritage site.

Beach face and berm morphodynamics fronting a coastal lagoon

This study documents two different modes of berm development: (I) vertical growth at spring tides or following significant beach cut due to substantial swash overtopping, and (2) horizontal progradation at neap tides through the formation of a proto-berm located lower and further seaward of the principal berm. Concurrent high-frequency measurements of bed elevation and the associated wave runup distribution reveal the details of each of these berm growth modes. In mode I sediment is eroded from the inner surf and lower swash zone where swash interactions are prevalent. The net transport of this sediment is landward only, resulting in accretion onto the upper beach face and over the berm crest. The final outcome is a steepening of the beach face gradient, a change in the profile shape towards concave and rapid vertical and horizontal growth of the berm. In mode 2 sediment is eroded from the lower two-thirds of the active swash zone during the rising tide and is transported both landward and seaward. On the falling tide sediment is eroded from the inner surf and transported landward to backfill the zone eroded on the rising tide. The net result is relatively slow steepening of the beach face, a change of the profile shape towards convex, and horizontal progradation through the formation of a neap berm. The primary factor determining which mode of berm growth occurs is the presence or absence of swash overtopping at the time of sediment accumulation on the beach face. This depends on the current phase of the spring-neap tide cycle, the wave runup height (and indirectly offshore wave conditions) and the height of the pre-existing berm. A conceptual model for berm morphodynamics is presented, based on sediment transport shape functions measured during the two modes of berm growth. (c) 2006 Elsevier B.V. All rights reserved.

(Quantum-) critical dynamics of magnetoelectric materials

In this thesis the critical dynamics of several magnetoelectric compounds at their phase transition were examined. Mostly measurements of the dielectric properties in the frequency range of below 1 Hz up to 5 GHz were employed to evaluate the critical exponents for both magnetic field and temperature-dependent measurements. Most of the materials that are part of this work show anomalous behavior, especially at very low temperatures where quantum fluctuations are of the order of or even dominate those induced thermally. This anomalous behavior manifests in different forms. In Dy2Ti2O7 we demonstrate the existence of electric dipoles on magnetic monopoles. Here the dynamics at the critical endpoint located at 0.36K and in a magnetic field of 1T parallel to the [111] direction are of special interest. At this critical endpoint the expected critical slowing down of the dynamics could not only not be observed but instead the opposite, critical speeding-up by several orders of magnitude, could be demonstrated. Furthermore, we show that the phase diagram of Dy2Ti2O7 in this field direction can be reproduced solely from the dynamical properties, for example the resonance frequency of the observed relaxation that is connected to the monopole movement. Away from this point of the phase diagram the dynamics are slowing-down with reduction of temperature as one would expect. Additional measurements on Y2Ti2O7, a structurally identical but non-magnetic material, show only slowing down with reduction of temperature and no additional features. A possible explanation for the observed critical speeding-up is a coherent movement of magnetic monopoles close to the critical field that increases the resonance frequency by reducing the damping of the process. LiCuVO4 on the other hand behaves normally at its phase transition as long as the temperature is higher than 0.4 K. In this temperature regime the dynamics show critical slowing-down analogous to classical ferroelectric materials. This analogy extends also towards higher frequencies where the permittivity displays a ‘dispersion’ minimum that is temperature-dependent but of the order of 2 GHz. Below 0.4K the observed behavior changes drastically. Here we found no longer relaxational behavior but instead an excitation with very low energy. This low energy excitation was predicted by theory and is caused by nearly gapless soliton excitations within the 1D Cu2+ chains of LiCuVO4. Finally, in TbMnO3 the dynamics of the phase transition into the multiferroic phase was observed at roughly 27 K, a much higher temperature compared to the other materials. Here the expected critical slowing-down was observed, even though in low-frequency measurements this transition into the ferroelectric phase is overshadowed by the so-called c-axis relaxation. Therefore, only frequencies above 1MHz could be used to determine the critical exponents for both temperatureand magnetic-field-dependent measurements. This was done for both the peak frequency as well as the relaxation strength. In TbMnO3 an electromagnetic soft-mode with small optical weight causes the observed fluctuations, similar to the case of multiferroic MnWO4.

A principal component approach to space-based gravitational wave astronomy

The current approach to data analysis for the Laser Interferometry Space Antenna (LISA) depends on the time delay interferometry observables (TDI) which have to be generated before any weak signal detection can be performed. These are linear combinations of the raw data with appropriate time shifts that lead to the cancellation of the laser frequency noises. This is possible because of the multiple occurrences of the same noises in the different raw data. Originally, these observables were manually generated starting with LISA as a simple stationary array and then adjusted to incorporate the antenna's motions. However, none of the observables survived the flexing of the arms in that they did not lead to cancellation with the same structure. The principal component approach is another way of handling these noises that was presented by Romano and Woan which simplified the data analysis by removing the need to create them before the analysis. This method also depends on the multiple occurrences of the same noises but, instead of using them for cancellation, it takes advantage of the correlations that they produce between the different readings. These correlations can be expressed in a noise (data) covariance matrix which occurs in the Bayesian likelihood function when the noises are assumed be Gaussian. Romano and Woan showed that performing an eigendecomposition of this matrix produced two distinct sets of eigenvalues that can be distinguished by the absence of laser frequency noise from one set. The transformation of the raw data using the corresponding eigenvectors also produced data that was free from the laser frequency noises. This result led to the idea that the principal components may actually be time delay interferometry observables since they produced the same outcome, that is, data that are free from laser frequency noise. The aims here were (i) to investigate the connection between the principal components and these observables, (ii) to prove that the data analysis using them is equivalent to that using the traditional observables and (ii) to determine how this method adapts to real LISA especially the flexing of the antenna. For testing the connection between the principal components and the TDI observables a 10x 10 covariance matrix containing integer values was used in order to obtain an algebraic solution for the eigendecomposition. The matrix was generated using fixed unequal arm lengths and stationary noises with equal variances for each noise type. Results confirm that all four Sagnac observables can be generated from the eigenvectors of the principal components. The observables obtained from this method however, are tied to the length of the data and are not general expressions like the traditional observables, for example, the Sagnac observables for two different time stamps were generated from different sets of eigenvectors. It was also possible to generate the frequency domain optimal AET observables from the principal components obtained from the power spectral density matrix. These results indicate that this method is another way of producing the observables therefore analysis using principal components should give the same results as that using the traditional observables. This was proven by fact that the same relative likelihoods (within 0.3%) were obtained from the Bayesian estimates of the signal amplitude of a simple sinusoidal gravitational wave using the principal components and the optimal AET observables. This method fails if the eigenvalues that are free from laser frequency noises are not generated. These are obtained from the covariance matrix and the properties of LISA that are required for its computation are the phase-locking, arm lengths and noise variances. Preliminary results of the effects of these properties on the principal components indicate that only the absence of phase-locking prevented their production. The flexing of the antenna results in time varying arm lengths which will appear in the covariance matrix and, from our toy model investigations, this did not prevent the occurrence of the principal components. The difficulty with flexing, and also non-stationary noises, is that the Toeplitz structure of the matrix will be destroyed which will affect any computation methods that take advantage of this structure. In terms of separating the two sets of data for the analysis, this was not necessary because the laser frequency noises are very large compared to the photodetector noises which resulted in a significant reduction in the data containing them after the matrix inversion. In the frequency domain the power spectral density matrices were block diagonals which simplified the computation of the eigenvalues by allowing them to be done separately for each block. The results in general showed a lack of principal components in the absence of phase-locking except for the zero bin. The major difference with the power spectral density matrix is that the time varying arm lengths and non-stationarity do not show up because of the summation in the Fourier transform.

Pulse shape measurements using single shot-frequency resolved optical gating for high energy (80 J) short pulse (600 fs) laser

Relevant to laser based electron/ion accelerations, a single shot second harmonic generation frequency resolved optical gating (FROG) system has been developed to characterize laser pulses (80 J, ∼600 fs) incident on and transmitted through nanofoil targets, employing relay imaging, spatial filter, and partially coated glass substrates to reduce spatial nonuniformity and B-integral. The device can be completely aligned without using a pulsed laser source. Variations of incident pulse shape were measured from durations of 613 fs (nearly symmetric shape) to 571 fs (asymmetric shape with pre- or postpulse). The FROG measurements are consistent with independent spectral and autocorrelation measurements. © 2010 American Institute of Physics.

Scattering-parameter measurements of laser diodes

An accurate and simple technique for measuring the input reflection coefficient and the frequency response of semiconductor laser diode chips is proposed and demonstrated. All the packaging parasitics could be obtained accurately using a calibrated probe, and the impedance of the intrinsic diode chip is deduced from the directly measured reflection coefficient. The directly measured impedance of a laser diode is affected strongly by the short bond wire. In the frequency response (S(2)1) measurements of semiconductor laser diode chips, the test fixture consists of a microwave probe, a submount, and a bond wire. The S-parameters of the probe could be determined using the short-open-match (SOM) method. Both the attenuation and the reflection of the test fixture have a strong influence on the directly measured frequency response, and in our proposed technique, the effect of test fixture is completely removed.

Absolute Atomic Oxygen Density Measurements by Two-Photon Absorption Laser-induced Fluorescence Spectroscopy in an RF-Excited Atmospheric Pressure Plasma Jet

The atmospheric pressure plasma jet is a capacitively coupled radio frequency discharge (13.56 MHz) running with a high helium flux (2m3 h-1) between concentric electrodes. Small amounts (0.5%) of admixed molecular oxygen do not disturb the homogeneous plasma discharge. The jet effluent leaving the discharge through the ring-shaped nozzle contains high concentrations of radicals at a low gas temperature—the key property for a variety of applications aiming at treatment of thermally sensitive surfaces. We report on absolute atomic oxygen density measurements by two-photon absorption laser-induced fluorescence (TALIF) spectroscopy in the jet effluent. Calibration is performed with the aid of a comparative TALIF measurement with xenon. An excitation scheme (different from the one earlier published) providing spectral matching of both the two-photon resonances and the fluorescence transitions is applied.

Kr-Ar laser Raman spectrometer for low temperature measurements /

A Czerny Mount double monochromator is used to measure Raman scattered radiation near 90" from a crystalline, Silicon sample. Incident light is provided by a mixed gas Kr-Ar laser, operating at 5145 A. The double monochromator is calibrated to true wavelength by comparison of Kr and Ar emission Une positions (A) to grating position (A) display [1]. The relationship was found to be hnear and can be described by, y = 1.219873a; - 1209.32, (1) where y is true wavelength (A) and xis grating position display (A). The Raman emission spectra are collected via C"*""*" encoded software, which displays a mV signal from a Photodetector and allows stepping control of the gratings via an A/D interface. [2] The software collection parameters, detector temperature and optics are optimised to yield the best quality spectra. The inclusion of a cryostat allows for temperatmre dependent capabihty ranging from 4 K to w 350 K. Silicon Stokes temperatm-e dependent Raman spectra, generally show agreement with Uterature results [3] in their frequency haxdening, FWHM reduction and intensity increase as temperature is reduced. Tests reveal that a re-alignment of the double monochromator is necessary before spectral resolution can approach literature standard. This has not yet been carried out due to time constraints.

Comparison of modal analysis results of laser vibrometry and nearfield acoustical holography measurements of an aluminum plate

Noise and vibration has long been sought to be reduced in major industries: automotive, aerospace and marine to name a few. Products must be tested and pass certain levels of federally regulated standards before entering the market. Vibration measurements are commonly acquired using accelerometers; however limitations of this method create a need for alternative solutions. Two methods for non-contact vibration measurements are compared: Laser Vibrometry, which directly measures the surface velocity of the aluminum plate, and Nearfield Acoustic Holography (NAH), which measures sound pressure in the nearfield, and using Green’s Functions, reconstructs the surface velocity at the plate. The surface velocity from each method is then used in modal analysis to determine the comparability of frequency, damping and mode shapes. Frequency and mode shapes are also compared to an FEA model. Laser Vibrometry is a proven, direct method for determining surface velocity and subsequently calculating modal analysis results. NAH is an effective method in locating noise sources, especially those that are not well separated spatially. Little work has been done in incorporating NAH into modal analysis.

Thermal and mechanical effects of different excitation modes based on low frequency laser modulation in optical hyperthermia

The low frequency modulation of the laser source (menor que30KHz) allows the generation of a pulsed signal that intermittently excites the gold nanorods. The temperature curves obtained for different frequencies and duty cycles of modulation but with equal average power and identical laser parameters, show that the thermal behavior in continuous wave and modulation modes is the same. However, the cell death experiments suggest that the percentage of death is higher in the cases of modulation. This observation allows us to conclude that there are other effects in addition to temperature that contribute to the cellular death. The mechanical effects like sound or pressure waves are expected to be generated from thermal expansion of gold nanorods. In order to study the behavior and magnitude of these processes we have developed a measure device based on ultrasound piezoelectric receivers (25KHz) and a lock-in amplifier that is able to detect the sound waves generated in samples of gold nanorods during laser irradiation providing us a voltage result proportional to the pressure signal. The first results show that the pressure measurements are directly proportional to the concentration of gold nanorods and the laser power, therefore, our present work is focused on determine the real influence of these effects in the cell death process.

High-brightness all semiconductor laser at 1.57 µm for space-borne lidar measurements of atmospheric carbon dioxide: device design and analysis of requirements

The availability of suitable laser sources is one of the main challenges in future space missions for accurate measurement of atmospheric CO2. The main objective of the European project BRITESPACE is to demonstrate the feasibility of an all-semiconductor laser source to be used as a space-borne laser transmitter in an Integrated Path Differential Absorption (IPDA) lidar system. We present here the proposed transmitter and system architectures, the initial device design and the results of the simulations performed in order to estimate the source requirements in terms of power, beam quality, and spectral properties to achieve the required measurement accuracy. The laser transmitter is based on two InGaAsP/InP monolithic Master Oscillator Power Amplifiers (MOPAs), providing the ON and OFF wavelengths close to the selected absorption line around 1.57 µm. Each MOPA consists of a frequency stabilized Distributed Feedback (DFB) master oscillator, a modulator section, and a tapered semiconductor amplifier optimized to maximize the optical output power. The design of the space-compliant laser module includes the beam forming optics and the thermoelectric coolers.The proposed system replaces the conventional pulsed source with a modulated continuous wave source using the Random Modulation-Continuous Wave (RM-CW) approach, allowing the designed semiconductor MOPA to be applicable in such applications. The system requirements for obtaining a CO2 retrieval accuracy of 1 ppmv and a spatial resolution of less than 10 meters have been defined. Envelope estimated of the returns indicate that the average power needed is of a few watts and that the main noise source is the ambient noise.

Soot measurements in steady and pulsed ethylene/air diffusion flames using Laser-Induced Incandescence

Combustion-generated carbon black nano particles, or soot, have both positive and negative effects depending on the application. From a positive point of view, it is used as a reinforcing agent in tires, black pigment in inks, and surface coatings. From a negative point of view, it affects performance and durability of many combustion systems, it is a major contributor of global warming, and it is linked to respiratory illness and cancer. Laser-Induced Incandescence (LII) was used in this study to measure soot volume fractions in four steady and twenty-eight pulsed ethylene diffusion flames burning at atmospheric pressure. A laminar coflow diffusion burner combined with a very-high-speed solenoid valve and control circuit provided unsteady flows by forcing the fuel flow with frequencies between 10 Hz and 200 Hz. Periodic flame oscillations were captured by two-dimensional phase-locked LII images and broadband luminosity images for eight phases (0° – 360°) covering each period. A comparison between the steady and pulsed flames and the effect of the pulsation frequency on soot volume fraction in the flame region and the post flame region are presented. The most significant effect of pulsing frequency was observed at 10 Hz. At this frequency, the flame with the lowest mean flow rate had 1.77 times enhancement in peak soot volume fraction and 1.2 times enhancement in total soot volume fraction; whereas the flame with the highest mean flow rate had no significant change in the peak soot volume fraction and 1.4 times reduction in the total soot volume fraction. A correlation (fvRe-1 = a + b·Str) for the total soot volume fraction in the flame region for the unsteady laminar ethylene flames was obtained for the pulsation frequency between 10 Hz and 200 Hz, and the Reynolds number between 37 and 55. The soot primary particle size in steady and unsteady flames was measured using the Time-Resolved Laser-Induced Incandescence (TIRE-LII) and the double-exponential fit method. At maximum frequency (200 Hz), the soot particles were smaller in size by 15% compared to the steady case in the flame with the highest mean flow rate.

Soot Measurements in Steady and Pulsed Ethylene/Air Diffusion Flames Using Laser-Induced Incandescence

Combustion-generated carbon black nano particles, or soot, have both positive and negative effects depending on the application. From a positive point of view, it is used as a reinforcing agent in tires, black pigment in inks, and surface coatings. From a negative point of view, it affects performance and durability of many combustion systems, it is a major contributor of global warming, and it is linked to respiratory illness and cancer. Laser-Induced Incandescence (LII) was used in this study to measure soot volume fractions in four steady and twenty-eight pulsed ethylene diffusion flames burning at atmospheric pressure. A laminar coflow diffusion burner combined with a very-high-speed solenoid valve and control circuit provided unsteady flows by forcing the fuel flow with frequencies between 10 Hz and 200 Hz. Periodic flame oscillations were captured by two-dimensional phase-locked LII images and broadband luminosity images for eight phases (0°- 360°) covering each period. A comparison between the steady and pulsed flames and the effect of the pulsation frequency on soot volume fraction in the flame region and the post flame region are presented. The most significant effect of pulsing frequency was observed at 10 Hz. At this frequency, the flame with the lowest mean flow rate had 1.77 times enhancement in peak soot volume fraction and 1.2 times enhancement in total soot volume fraction; whereas the flame with the highest mean flow rate had no significant change in the peak soot volume fraction and 1.4 times reduction in the total soot volume fraction. A correlation (ƒv Reˉ1 = a+b· Str) for the total soot volume fraction in the flame region for the unsteady laminar ethylene flames was obtained for the pulsation frequency between 10 Hz and 200 Hz, and the Reynolds number between 37 and 55. The soot primary particle size in steady and unsteady flames was measured using the Time-Resolved Laser-Induced Incandescence (TIRE-LII) and the double-exponential fit method. At maximum frequency (200 Hz), the soot particles were smaller in size by 15% compared to the steady case in the flame with the highest mean flow rate.