Graduate School

Structural analysis of materials with x-ray absorption and emission spectroscopy and microscopy

This course is part of the programme:
Materials (Third Level)

Objectives and competences

The primary goal of this course is to give students the knowledge of modern synchrotron radiation (SR) x-ray absorption and emission spectroscopic methods EXAFS and XANES for the autonomous characterization of the atomic and molecular structure of different materials including in-opearndo and in-situ mode, and for 2D and 3D mapping of elements with micro-XRF, particularly on plant tissues on subcellular level.

Students gain necessary competences to prepare competitive scientific project to obtain beamtime in different synchrotron radiation laboratories, to prepare and perform experiments with synchrotron radiation, and to quantitatively analyse measurements and interpret the results.

Prerequisites

The primary goal of this course is to give students the knowledge of modern synchrotron radiation (SR) x-ray absorption and emission spectroscopic methods EXAFS and XANES for the autonomous characterization of the atomic and molecular structure of different materials including in-opearndo and in-situ mode, and for 2D and 3D mapping of elements with micro-XRF, particularly on plant tissues on subcellular level.

Students gain necessary competences to prepare competitive scientific project to obtain beamtime in different synchrotron radiation laboratories, to prepare and perform experiments with synchrotron radiation, and to quantitatively analyse measurements and interpret the results.

Content (Syllabus outline)

    • Interaction of x-rays with matter
    • X-ray absorption spectroscopy (methods EXAFS and XANES)
    • X-ray fluorescence spectroscopy
    • X-ray absorption measurements with synchrotron radiation in transmission and fluorescence mode, X-ray detectors, (micro)focusing X-ray optic elements, confocal optics, in-situ and in-operando experiments;
    • 2D and 3D mapping of elements with micro and nano spatial resolution
    • Micro-spectroscopy (combination of XAS and micro focusing of SR X-ray beam)
    • Quantitative analysis of XRF spectra
    • Numerical analysis of EXAFS and XANES spectra
    • Advanced analytical methods (parallel multi-edge fitting of several EXAFS spectra, linear combination fits and PCA in XANES analysis
    • Atomic absorption background in XAS spectra.
    • Typical examples of structure analysis with XANES and EXAFS: in operando analysis of Li-ion and Li-sulphur batteries, in situ XAS analysis of catalysts, structural analysis of nanomaterials, liquids, strongly disordered materials, dopants in crystalline materials, samples from cultural heritage
    • Micro XAS and XRF analysis of environmental and biological samples on subcellular level, metal pollutants and essential elements in plant tissues

Intended learning outcomes

Knowledge and understanding:

Students learn the principles of different x-ray spectroscopic methods (EXAFS, XANES, micro-XAFS, …) and emission methods (XRF in micro-XRF, nano-XRF) and their use in practice as structural tools. Students gain know-how on the whole process from preparation and realisation of XAS and XRF experiments with broad beam and micro or nano-focused beam at synchrotron radiation laboratories, to the analysis and finally the interpretation of XAS and XRF spectra and 2D and 3D mapping of elements on sub-micron level. With practical work on examples from research practice using up-to-date XAS and XRF software, they learn advanced techniques of the evaluation and interpretation of obtained XANES and EXAFS results (parallel multi-edge fitting of several EXAFS spectra, linear combination fits and PCA in XANES analysis). They know typical sources of systematic errors in absorption and emission spectra (self-absorption in emission, inhomogeneity of samples in transmission, atomic absorption background in EXAFS spectra, radiation damage of samples during measurements). They obtain know-how necessary to prepare a good proposal for beamtime and to perform successful experiments at XAS beamlies at different synchrotron radiation facilities. Students learn which combination of spectroscopic methods is optimal for the analysis of specific material properties.

Readings

  • I. Arčon, Introduction to XANES and EXAFS analysis. Nova Gorica: [I. Arčon], 2008. 35 str., ilustr. [COBISS.SI-ID 933883]
  • I. Arčon, X-ray absorption spectroscopy : a practical guide to structural analysis of materials with EXAFS and XANES analysis. Nova Gorica: [I. Arčon], 2008. 51 str., ilustr. [COBISS.SI-ID 934139]
  • G. Bunker, “Introduction to XAFS: A Practical Guide to X-ray Absorption Fine Structure Spectroscopy”, Cambridge University Press, 2010
  • X-ray absorption spectroscopy, ed. D.C. Konnigsberger and R. Prins, Wiley&Sons, 1988
  • J. J. Rehr, R. C. Albers, Theoretical approaches to x-ray absorption fine structure, Reviews of Modern Physics, Vol. 72, No. 3, July 2000, 621-654
  • B. Beckhoff, B. Kanngiesser, N. Langhoff R. Wedell H. Wolff, Handbook of Practical X-Ray Fluorescence Analysis, Springer-Verlag Berlin Heidelberg 2006, ISBN-10 3-540-28603-9 Springer Berlin, Heidelberg
  • J. Wong, F.W. Lytle, R. P. Messmer, D.H. Maylotte, K-edge spectra of slected vanadium compounds, Phys. Rev. B 30 (1984) 5596 – 5610
  • Katarina Vogel-Mikuš, Iztok Arčon, Peter Kump, Primož Pelicon, Marijan Nečemer, Primož Vavpetič, Špela Koren, Marjana Regvar, Analytical tools for exploring metal accumulation and tolerance in plants.

Phytotechnologies : remediation of environmental contaminants. Boca Raton (FL): Taylor & Francis, cop. V: Naser A. Anjum, (ed.). (2013) 443-495

  • K. Vogel-Mikuš, P. Kump, M. Nečemer, P. Pelicon, I. Arčon, P. Pongrac, B. Povh, M. Regvar, Quantitative analyses of trace elements in environmental samples : options and (im)possibilities. Soil heavy metals, (Soil biology, 19). Heidelberg [etc.]: Springer, 2010, str. 113-138.
  • V. Kaučič, N. Zabukovec Logar, I. Arčon,. Characterisation of microporous and mesoporous solids using complementary diffraction and X-ray absorption spectroscopic techniques. V: Characterization techniques for zeolites and related materials : state of the art and recent developments. [S.l.: s.n.], 2008, str. 91-123. 2nd FEZA school 2008, Universite Pierre et marie Curie, Paris, September 1-2, 2008 [COBISS.SI-ID 3992602]
  • I. Arčon, tutorials on the web: http://www.p-ng.si/~arcon/xas and http://www.ung.si/~arcon/xas-si and

http://www.ung.si/~arcon/xas/students

  • IFEFFIT software and documentation for XAS analysis: http://cars.uchicago.edu/ifeffit/Ifeffit
  • DEMETER software and documentation (XAS software) http://bruceravel.github.com/demeter/
  • FEFF documentations: http://leonardo.phys.washington.edu/feff/
  • PyMCA software for XRF analysis: http://pymca.sourceforge.net/

Assessment

During the course students prepare individual projects on X-ray absorption and emission spectroscopy and on quantitative EXAFS and XANES analysis on real data from research practice. At the end of the course they prepare a final project, i.e. experiment proposal for beamtime at a selected synchrotron X-ray absoprtion beamline. All projects are prepared in a written form and defended orally in an open discussion with professor and students. (50/50)

Lecturer's references

Prof. dr. Iztok Arčon is a full professor for the field of physics, employed at the University of Nova Gorica. His main research filed is analysis of atomic and molecular structure of new materials and analysis of environmental pollution (soil, water and plants) with X-ray absorption spectroscopy with synchrotron radiation. In 2006 he received national “Zois award” for outstanding achievements in the field of X-ray absorption spectroscopy.

Selected publications

1. ARČON, Iztok, PICCOLO, Oreste, PAGANELLI, Stefano, BALDI, Franco. XAS analysis of a nanostructured iron polysaccharide produced anaerobically by a strain of Klebsiella oxytoca. Biometals, ISSN 0966-0844, 2012, vol. 25, no. 5, str. 875-881, doi: 10.1007/s10534-012-9554-6. [COBISS.SI-ID

2264827].

2. DOMINKO, Robert, ARČON, Iztok, KODRE, Alojz, HANŽEL, Darko, GABERŠČEK, Miran. In-situ XAS study on Li[sub]2MnSiO[sub]4 and Li[sub]2FeSiO[sub]4 cathode materials. V: Selected papers presented at the 14th international meeting on lithium batteries : Tianjin, China, 22 -28 June 2008 :

IMLB-2008, (Journal of power sources, ISSN 0378-7753, Vol. 189, Issue 1,

2009). Lausanne: Elsevier, 2009, vol. 189, no. 1, str. 51-58, doi: 10.1016/j.jpowsour.2008.11.077. [COBISS.SI-ID 1073915].

3. VALANT, Matjaž, KOLODIAZHNYI, Taras, ARČON, Iztok, AGUESSE, Frederic, AXELSSON, Anna-Karin, ALFORD, Neil McN. The origin of magnetism in Mn-doped SrTiO [sub] 3. Advanced functional materials, ISSN 1616-301X, maj 2012, vol. 22, no. 10, str. 2114-2122. [COBISS.SI-ID 2265083].

4. ARČON, Iztok, KOLAR, Jana, KODRE, Alojz, HANŽEL, Darko, STRLIČ, Matija. XANES analysis of Fe valence in iron gall inks. X-ray spectrometry, ISSN 0049-8246, 2007, vol. 36, str. 199-205. [COBISS.SI-ID 665339].

5. VOGEL-MIKUŠ, Katarina, ARČON, Iztok, KUMP, Peter, PELICON, Primož, NEČEMER, Marijan, VAVPETIČ, Primož, KOREN, Špela, REGVAR, Marjana. Analytical tools for exploring metal accumulation and tolerance in plants. V: ANJUM, Naser A. (ur.). Phytotechnologies : remediation of environmental

contaminants. Boca Raton (FL): Taylor & Francis, cop. 2013, str. 443-495,

ilustr. [COBISS.SI-ID 2671439].

University course code: 3FIi24*

Year of study: 1

Lecturer:

ECTS: 9

Workload:

  • Lectures: 40 hours
  • Exercises: 20 hours
  • Individual work: 210 hours

Course type: elective

Languages: slovene/english

Learning and teaching methods:
lectures. exercises on state of the art software for the analysis of xasand xrf spectra on real data from research practice, under supervision of the the lecturer responsible for the course. individual project work under supervision of the lecturer responsible for the course. presentation and interpreation of project results to other students in open discussion under supervision of the lecturer responsible for the course. journal club – discussion of published research articles on the selected xas and xrf topics assessment: during the course students prepare individual projects on x-ray absorption and emission spectroscopy and on quantitative exafs and xanes analysis on real data from research practice. at the end of the course they prepare a final project, i.e. experiment proposal for beamtime at a selected synchrotron x-ray absoprtion beamline. all projects are prepared in a written form and defended orally in an open discussion with professor and students.