Dr. Jacob Filik Profile

Dr. Jacob Filik

at Diamond Light Source Ltd

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Proceedings Article | 5 October 2023 Open Access

PyCSFex: an extensible Python three package for calculating x-ray structure factors in complex crystals

John Sutter, James Pittard, Jacob Filik, Alfred Q. Baron

Proceedings Volume 12697, 126970A (2023) https://doi.org/10.1117/12.2676361

KEYWORDS: Chemical species

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Near-perfect diffracting crystals have many uses in x-ray optics including as monochromators, energy analyzers, and phase retarders. The usefulness of a particular Bragg reflection is often related to its angular acceptance and efficiency, as is determined by the reflection’s structure factor. Silicon crystals, which belong to the same face-centered cubic space group 𝐹𝑑3̅𝑚 as germanium and diamond, are readily available in large and highly pure ingots. Combined with their high thermal conductivity and low thermal expansion, this makes them suitable for synchrotron x-ray beamlines. However, less symmetric trigonal crystals such as sapphire, lithium niobate, and α-quartz offer a better choice of high-energy-resolution Bragg reflections near backscattering with less likelihood of parasitic Bragg reflections. Because these crystals’ atoms vibrate anisotropically and shift relative to each other with temperature, the temperature dependence of their structure factors is not a given by a simple Debye-Waller factor. Also, many crystal structures may be described by several different conventions of origin and lattice vectors. A Python three software package, PyCSFex, is presented here for the rapid calculation of large numbers of structure factors of any crystal described in any convention. It can run on its own or as part of an already existing software package. Users can extend the package to new crystals by writing their own material files. α-Quartz is chosen as an example because it has already been successfully used in backscattering x-ray energy analyzers and presents the complexities previously mentioned.

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Proceedings Article | 8 February 2008 Paper

Raman point mapping of tear ferning patterns

Jacob Filik, Nicholas Stone

Proceedings Volume 6853, 685309 (2008) https://doi.org/10.1117/12.786441

KEYWORDS: Proteins, Raman spectroscopy, Image processing, Urea, Coating, Principal component analysis, Eye, Analytical research, Biological research, Biomedical optics

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This study attempts to combine the tear ferning test and the drop coating deposition Raman spectroscopy (DCDRS) technique to analyze the biochemical composition of human tear fluid from healthy volunteers. DCDRS has been shown to be a highly reproducible and sensitive method of obtaining Raman spectra from low concentration protein solutions making it ideal for the analysis of tear fluid. On drying, tear samples were found to produce ring-shaped patterns, which are characteristic of the DCDRS technique, with additional fern-like structures produced inside the rings. The biochemical composition of the each drying pattern was studied by Raman point mapping and principal components analysis. Assignment of high-signal-to-noise tear spectra showed that tear proteins, urea, bicarbonate and lipid components were all present in the dried tear drop. Comparing an image time series of the drying process with the biochemical distributions from the Raman point map revealed the order of biochemical deposition in the drying pattern. The combination of DCDRS and the tear ferning test shows enough promise to be further studied as a near-patient technique for assisting the diagnosis of ocular infection, but further work is required to validate the technique.

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