Data analysis in extended x-ray-absorption fine structure: Determination of the background absorption and the threshold energy

Two approaches for the determination of the background absorption (μ_0) in the extended x-ray-absorption fine structure (EXAFS) are presented. Both methods, experimental and computational, take advantage of the damping of the EXAFS amplitude resulting from the convolution with Gaussian functions of different widths. In the experimental method two or more spectra are collected with the use of different spectrometer slit widths, resulting in spectra of different resolutions for the same sample. In the computational approach the convolution is accomplished via a convolution algorithm. The intersection points of the resulting spectra are used to generate μ_0. At the absorption edge, the spectra intersect at a unique point, which is shown to be a measure of the threshold energy, E_0. Illustration of the two methods for background removal is given for a copper-foil sample. The computational approach is superior to the experimental method of damping the EXAFS spectra to give μ_0

Holistic spectroscopy: complete reconstruction of a wide-field, multiobject spectroscopic image using a photonic comb

The primary goal of Galactic archaeology is to learn about the origin of the Milky Way from the detailed chemistry and kinematics of millions of stars. Wide-field multifibre spectrographs are increasingly used to obtain spectral information for huge samples of stars. Some surveys (e.g. GALAH) are attempting to measure up to 30 separate elements per star. Stellar abundance spectroscopy is a subtle art that requires a very high degree of spectral uniformity across each of the fibres. However, wide-field spectrographs are notoriously non-uniform due to the fast output optics necessary to image many fibre outputs on to the detector. We show that precise spectroscopy is possible with such instruments across all fibres by employing a photonic comb – a device that produces uniformly spaced spots of light on the CCD to precisely map complex aberrations. Aberrations are parametrized by a set of orthogonal moments with ∼100 independent parameters. We then reproduce the observed image by convolving high-resolution spectral templates with measured aberrations as opposed to extracting the spectra from the observed image. Such a forward modelling approach also trivializes some spectroscopic reduction problems like fibre cross-talk, and reliably extracts spectra with a resolution ∼2.3 times above the nominal resolution of the instrument. Our rigorous treatment of optical aberrations also encourages a less conservative spectrograph design in the future

Advanced methods in fourier transform ion cyclotron resonance mass spectrometry

Mass spectrometry (MS) is a powerful analytical technique used to characterize various compounds by measuring the mass-to-charge ratio (m/z). Among different types of mass analyzers, Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) is the instrument of choice for those working at the forefront of research, as it offers incomparable mass accuracy, resolving power, and the highest flexibility for hybrid instrumentation and fragmentation techniques. The FT-ICR MS requires professional and careful tuning to achieve its superior performance. Our work aims to review, develop and apply advanced methods to improve the data quality of FT-ICR and push the limits of the instrument. FT-ICR spectrometry has been limited to the magnitude-mode for 40 years due to the complexity of the phase-wrapping problem. However, it is well known that by correcting phase of the data, the spectrum can be plotted in the absorption-mode with a mass resolving power that is as much as two times higher than conventional magnitude-mode. Based on the assumption that the frequency sweep excitation produces a quadratic accumulation in an ion’s phase value, a robust manual method to correct all ions’ phase shifts has been developed, which allows a broadband FT-ICR spectrum to be plotted in the absorption-mode. The developed phasing method has then been applied to a large variety of samples (peptides, proteins, crude oil), different spectral acquisition-mode (broadband, narrowband), and different design of ICR cells (Infinity cell, ParaCell) to compare the performance with the conventional magnitude-mode spectra. The outcome shows that, by plotting the absorption-mode spectrum, not only is the spectral quality improved at no extra cost, but the number of detectable peaks is also increased. Additionally, it has been found that artifactual peaks, such as noise or harmonics in the spectrum can be diagnosed immediately in the absorption-mode. Given the improved characteristics of the absorption-mode spectrum, the following research was then focused on a data processing procedure for phase correction and the features of the phase function. The results demonstrate that in the vast majority of cases, the phase function needs to be calculated just once, whenever the instrument is calibrated. In addition, an internal calibration method for calculating the phase function of spectra with insufficient peak density across the whole mass range has been developed. The above research is the basis of the Autophaser program which allows spectra recorded on any FT-ICR MS to be phase corrected in an automated manner

Fiber Laser Based Nonlinear Spectroscopy

To date, nonlinear spectroscopy has been considered an expensive technique and confined mostly to experimental laboratory settings. Over recent years, optical-fiber lasers that are highly reliable, simple to operate and relatively inexpensive have become commercially available, removing one of the major obstacles to widespread utilization of nonlinear optical measurement in biochemistry. However, fiber lasers generally offer relatively low output power compared to lasers traditionally used for nonlinear spectroscopy, and much more careful design is necessary to meet the excitation power thresholds for nonlinear signal generation. On the other hand, reducing the excitation intensity provides a much more suitable level of user-safety, minimizes damage to biological samples and reduces interference with intrinsic chemical processes. Compared to traditional spectroscopy systems, the complexity of nonlinear spectroscopy and imaging instruments must be drastically reduced for them to become practical. A nonlinear spectroscopy tool based on a single fiber laser, with electrically controlled wavelength-tuning and spectral resolution enhanced by a pulse shaping technique, will efficiently produce optical excitation that allows quantitative measurement of important nonlinear optical properties of materials. The work represented here encompasses the theory and design of a nonlinear spectroscopy and imaging system of the simplest architecture possible, while solving the difficult underlying design challenges. With this goal, the following report introduces the theories of nonlinear optical propagation relevant to the design of a wavelength tunable system for nonlinear spectroscopy applications, specifically Coherent Anti-Stokes Spectroscopy (CARS) and Förster Resonance Energy Transfer (FRET). It includes a detailed study of nonlinear propagation of optical solitons using various analysis techniques. A solution of the generalized nonlinear Schrödinger equation using the split-step Fourier method is demonstrated and investigation of optical soliton propagation in fibers is carried out. Other numerical methods, such as the finite difference time domain approach and spectral-split step Fourier methods are also described and compared. Numerical results are contrasted with various measurements of wavelength shifted solitons. Both CARS and FRET test-bed designs and experiments are presented, representing two valuable biochemical measurement applications. Two-photon excitation experiments with a simplified calibration process for quantitative FRET measurement were conducted on calmodulin proteins modified with fluorescent dyes, as well as modified enhanced green fluorescent protein. The resulting new FRET efficiency measurements showed agreement with those of alternative techniques which are slower and can involve destruction of the sample. In the second major application of the nonlinear spectroscopy system, CARS measurement with enhanced spectral resolution was conducted on cyclohexane as well as on samples of mouse brain tissue containing lipids with Raman resonances. The measurements of cyclohexane verified the ability of the system to precisely determine its Raman resonances, thus providing a benchmark within a similar spectral range for biological materials which have weaker Raman signal responses. The improvement of spectral resolution (resonance frequency selectivity), was also demonstrated by measuring the closely-spaced resonances of cyclohexane. Finally, CARS measurements were also made on samples of mouse brain tissue which has a lipids-based Raman signature. The CARS spectrum of the lipid resonances matched well with other cited studies. The imaging of mouse brain tissue with Raman resonance contrast was also partially achieved, but it was hindered by low signal to noise ratio and limitations of the control hardware that led to some dropout of the CARS signal due to power coupling fluctuations. Nevertheless, these difficulties can be straightforwardly addressed by refinement of the wavelength tuning electronics. In conclusion, it is hoped that these efforts will lead to greater accessibility and use of CARS, FRET and other nonlinear spectral measurement instruments, in line with the promising advances in optics and laser technology

The quest for the solar g modes

Solar gravity modes (or g modes) -- oscillations of the solar interior for which buoyancy acts as the restoring force -- have the potential to provide unprecedented inference on the structure and dynamics of the solar core, inference that is not possible with the well observed acoustic modes (or p modes). The high amplitude of the g-mode eigenfunctions in the core and the evanesence of the modes in the convection zone make the modes particularly sensitive to the physical and dynamical conditions in the core. Owing to the existence of the convection zone, the g modes have very low amplitudes at photospheric levels, which makes the modes extremely hard to detect. In this paper, we review the current state of play regarding attempts to detect g modes. We review the theory of g modes, including theoretical estimation of the g-mode frequencies, amplitudes and damping rates. Then we go on to discuss the techniques that have been used to try to detect g modes. We review results in the literature, and finish by looking to the future, and the potential advances that can be made -- from both data and data-analysis perspectives -- to give unambiguous detections of individual g modes. The review ends by concluding that, at the time of writing, there is indeed a consensus amongst the authors that there is currently no undisputed detection of solar g modes.Comment: 71 pages, 18 figures, accepted by Astronomy and Astrophysics Revie