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Dictionary learning in Fourier-transform scanning tunneling spectroscopy.

ABSTRACT: Modern high-resolution microscopes are commonly used to study specimens that have dense and aperiodic spatial structure. Extracting meaningful information from images obtained from such microscopes remains a formidable challenge. Fourier analysis is commonly used to analyze the structure of such images. However, the Fourier transform fundamentally suffers from severe phase noise when applied to aperiodic images. Here, we report the development of an algorithm based on nonconvex optimization that directly uncovers the fundamental motifs present in a real-space image. Apart from being quantitatively superior to traditional Fourier analysis, we show that this algorithm also uncovers phase sensitive information about the underlying motif structure. We demonstrate its usefulness by studying scanning tunneling microscopy images of a Co-doped iron arsenide superconductor and prove that the application of the algorithm allows for the complete recovery of quasiparticle interference in this material.

SUBMITTER: Cheung SC

PROVIDER: S-EPMC7044214 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Dictionary learning in Fourier-transform scanning tunneling spectroscopy.

Cheung Sky C SC Shin John Y JY Lau Yenson Y Chen Zhengyu Z Sun Ju J Zhang Yuqian Y Müller Marvin A MA Eremin Ilya M IM Wright John N JN Pasupathy Abhay N AN

Nature communications 20200226 1

Modern high-resolution microscopes are commonly used to study specimens that have dense and aperiodic spatial structure. Extracting meaningful information from images obtained from such microscopes remains a formidable challenge. Fourier analysis is commonly used to analyze the structure of such images. However, the Fourier transform fundamentally suffers from severe phase noise when applied to aperiodic images. Here, we report the development of an algorithm based on nonconvex optimization that ...[more]

PMID: 32102995

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Project description:Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of a given sample, as bacterial cells, induced by the absorption of infrared radiation. This technique has been largely used for the study of pathogenic species, especially in the clinical field, and has been proposed also for the typing at different subspecies levels. The high throughput, speed, low cost, and simplicity make FTIR spectroscopy an attractive technique also for industrial applications, in particular, for probiotics. The aim of this study was to compare FTIR spectroscopy with established genotyping methods, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS), and multilocus sequence typing (MLST), in order to highlight the FTIR spectroscopy potential discriminatory power at strain level. Our study focused on bifidobacteria, an important group of intestinal commensals generally recognized as probiotics. For their properties in promoting and maintaining health, bifidobacteria are largely marketed by the pharmaceutical, food, and dairy industries. Strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium animalis subsp. lactis were taken into consideration together with some additional type strains. For B. longum subsp. longum, it was possible to discriminate the strains with all the methods used. Although two isolates were shown to be strictly phylogenetically related, constituting a unique cluster, based on PFGE, WGS, and MLST, no clustering was observed with FTIR. For B. animalis subsp. lactis group, PFGE, WGS, and MLST were non-discriminatory, and only one strain was easily distinguished. On the other hand, FTIR discriminated all the isolates one by one, and no clustering was observed. According to these results, FTIR analysis is not only equivalent to PFGE, WGS, and MLST, but also for some strains, in particular, for B. animalis subsp. lactis group, more informative, being able to differentiate strains not discernible with the other two methods based on phenotypic variations likely deriving from certain genetic changes. Fourier transform infrared spectroscopy has highlighted the possibility of using the cell surface as a kind of barcode making tracing strains possible, representing an important aspect in probiotic applications. Furthermore, this work constitutes the first investigation on bifidobacterial strain typing using FTIR spectroscopy.

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Dictionary learning in Fourier-transform scanning tunneling spectroscopy.

Publications

Dictionary learning in Fourier-transform scanning tunneling spectroscopy.

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