AG Umwelt- und Bodenchemie


Available topic for master thesis

Use of Atomic force microscopy (AFM) for soil aggregates with complementary chemical info obtained by NanoSIMS


Various important physicochemical interactions occur in soil systems at the nano and micro scale and potentially affect the soil properties and functions at the landscape. The molecular interactions in soil microaggregates are believed to play a fundamental role for the distribution and preservation of some important elements including carbon and nutrients. Both the composition as well as the spatial organisation of the soil organic matter (SOM) in the soil matrix are strongly linked to the aggregate stability. Atomic force microscopy (AFM) is proven to be a powerful tool for the study of biological systems at the nano scale under different environmental conditions and temperatures. Nanoscale secondary ion mass spectrometry (NanoSIMS) is used to acquire measurements of the elemental and isotopic composition of a sample with nanoscale resolution which is still less than the one offered by AFM.

In cooperation with Technical University of Munich (TUM), School of Life Sciences, NanoSIMS and AFM will be applied to soil aggregates to pioneer soil nanoscience. We offer a Master Thesis with the following tasks:

To do

  1. Based on literature review on advanced microscopic and spectrometric techniques for soil, formulate a hypothesis for the use of AFM and NanoSIMS for soil aggregates
  2. Optimize fixation of soil aggregates < 20-40 µm on Si or GaAs wafer for AFM scans and choose areas fitting to AFM scans based on laser topography measurements (pre-select ROIs)
  3. Standardize method for mapping soil aggregate surface with high spatial resolution using AFM (selection of probe, scan parameters, etc.)
  4. Run scans of a number of regions of interest (ROIs) of soil aggregates and check for local areas occupied with SOM
  5. Do AFM Force spectroscopy at mineral dominated areas and SOM dominated areas
  6. Record coordinates to allow relocating the same AFM studied areas by NanoSIMS (later conducted in TUM (not by the master student)).
  7. Analyze the AFM images and Force curves using Nanoscope software and extract AFM images and quantitative data (shape, adhesion, stiffness, roughness, deformation and InPhase )
  8. Write Master Thesis combining AFM physical data and NanoSIMS chemical data.

Besides, it might be needed to process the soil samples with scanning electron microscopy (SEM) and sessile drop contact angle to get insights into the samples microstructure and wettability.


First of all, very high motivation&patience to learn AFM and extend the experience for the sturdy of the “complex” soil aggregates. Here, basic knowledge of AFM and its physical concepts is an advantage. The ability to work independently and having basic to good knowledge of statistical software (e.g., R) is needed. Background in soil physics, soil chemistry, or environmental sciences.

Related work

Gazze, S. A., et al. "Organic matter identifies the nano-mechanical properties of native soil aggregates." Nanoscale 10.2 (2018): 520-525.

Interested? Please Contact:

Abd Alaziz Abu Quba
Environmental and Soil Chemistry Group
iES Institute for Environmental Sciences
Universität Koblenz-Landau
Fortstrasse 7, 76829 Landau
+49 6341 280 31564

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