Nanoscale Microscopy and Spectroscopy

The Ruggeri Lab and team work to develop and apply transformative microscopy and spectroscopic technologies to open a new research front and window of observation in Chemistry and Biology. We apply advanced nanoscale imaging, mechanical and chemical spectroscopy to study biomolecular process in life and disease at the single molecule scale, as well as characterising advanced functional surfaces and materials.

Open Positions and Opportunities

We welcome applications from enthusiastic and Bachelors, Masters and PhDs students, as well as post-doctoral researchers who want to apply for national and international funding.

Please contact Dr. Francesco Simone Ruggeri (, and include a cover letter and CV.

Short Bio – Francesco Simone Ruggeri, Ph.D.

At the end of 2020, Francesco Simone Ruggeri has joined as Assistant Professor the chair groups of Organic Chemistry and Physical Chemistry of Wageningen University.

He holds a PhD in biophysics obtained in 2015 at the École Polytechnique Fédérale de Lausanne (EPFL) in Switzerland, where he acquired a strong expertise on scanning probe microscopy and single molecule methods. He has also acquired deep expertise in scanning probe microscopy, surface science, spectroscopy, data analysis, image processing and single particle characterisation.

Before his appointment in Wageningen, he has completed his independent Junior Research Fellowship at the Darwin College and his post-doctoral research at the Department of Chemistry & Centre for Misfolding disease at University of Cambridge (UK).

In his previous research, he has developed and applied of single molecule biophysical approaches, such as infrared nanospectroscopy, in combination with microfluidics, to study the chemical and structural properties of biological systems that are challenging to access using conventional bulk biophysical methods (Nature Nanotechnology, 2020; ACS Nano, 2020; Nucleic Acid Research, 2019; Nature Communications, 2019 & 2018 & 2017; PNAS, 2018; Nature Chemistry, 2018; Cell, 2018). Furthermore, he has first demonstrated the application of peak-force tapping mode and of infrared nanospectroscopy (AFM-IR) to correlate the nanomechanical, chemical and structural properties of biological samples at the nanoscale in air and liquid environment.

As major advance in the field of microscopy and spectroscopy, he has also demonstrated that infrared nanospectroscopy is capable to acquire the chemical fingerprint and secondary structure of biological samples in native liquid environments (ACS Nano, 2018) and at the single biomolecule scale (Nature Communications, 2020).

Overall, Dr. Ruggeri´s approach has brought new insights into the formation and structural characterization of misfolding of proteins and their correlation with the onset of neurodegenerative disorders.

The objective of his present and future research is the development and application of novel Physical methods at the interface with Chemistry and Biology. He will continuously push the boundaries of the nanoscale microscopy and spectroscopy to shed light on the molecular processes underlying life, cell function and disease, as well as study advanced functional surfaces and biomaterials.

Selected Publications

Google Scholar:

  • Lobanova E., Whiten D., Ruggeri F.S., Chris Taylor, Antonina Kouli, Zengjie Xia, Derya Emin, Yu P Zhang, Jeff Y L Lam, Caroline H Williams-Gray, David Klenerman, Imaging protein aggregates in the serum and cerebrospinal fluid in Parkinson’s disease, Brain, 2022, awab306,
  • Ruggeri F.S. # (corresponding), Habchi J., Chia S., Horne R., Vendruscolo M., Knowles T.P.J. Infrared nanospectroscopy reveals the molecular interaction fingerprint of an aggregation inhibitor with single Aβ42 oligomers, Nature Comm., 2021, 12(1), 1-9,
  • Daniel E. Otzen, Morten S. Dueholm, Zahra Najarzadeh, Tuomas P. J. Knowles, Francesco Simone Ruggeri, In situ Sub‐Cellular Identification of Functional Amyloids in Bacteria and Archaea by Infrared Nanospectroscopy, Small Methods, 2021.
  • Ruggeri F.S.#, Habchi J., Chia S., Vendruscolo M., Knowles T.P.J., Nature Communications, Infrared nanospectroscopy reveals the molecular interaction fingerprint of an aggregation inhibitor with single Aβ42 oligomers, 2021.
    • Ruggeri F.S.#, Mannini B., Schmidt R., Vendruscolo M., Knowles T.P.J. Single Molecule Secondary Structure Determination of Protein through Infrared Absorption Nanospectroscopy, Nature Communications, 2020.
  • Ruggeri F.S., Flagmeier P., Kumita J., Meisl G., Knowles T.P.J., Dobson C. M., The influence of pathogenic mutations in α-synuclein on kinetic mechanisms and structural characteristics of amyloid fibrils, ACS Nano, 2020.
  • Shen Y., Ruggeri F.S., Vigolo D., Kamada A., Qamar S., Levin A., Iserman C., Alberti S., St George-Hyslop P., Biomolecular condensates undergo a generic shear-mediated liquid-to-solid transition, Nature Nanotechnology, 2020.
  • Lipiec E., Ruggeri F.S., Benadiba C. Borkowska A., Kobierski J., Miszczyk J., Wood B., Deacon G., Kulik A., Dietler G. and Kwiatek W., Infrared nano-spectroscopic mapping of a single metaphase chromosome, Nucleic Acid Research, 2019.
  • Ruggeri F.S., Charmet J., Kartanas T., Peter Q., Habchi J., Vendruscolo M., Dobson C.M., Knowles T.P.J., Microfluidic deposition for resolving single molecule protein architecture and heterogeneity. Nature Communications, 2018.
  • Ruggeri F.S.#, Benedetti F., Knowles T.P.J., Lashuel H., Sekatskii S., Dietler G., Identification and nanomechanical characterization of the fundamental single-strand protofilaments of amyloid α-synuclein fibrils. PNAS, 2018.
  • Ramer G.*, Ruggeri F.S.*, Levin A., Knowles T.P.J., Centrone A., Determination of polypeptide conformation in water with nanoscale infrared spectroscopy. ACS Nano, 2018.
  • Qamar S.*, Wang G. *, Randle S. *, Ruggeri F.S. *, Varela J.*, Qiaojin Lin J., Phillips E.C., Miyashita A., Williams D., Meadows W., Ferry R., Dardov J.V., Tartaglia G., Farrer L.A., Kaminski G.S., Kaminski C., Holt C.E., Fraser P., Schmitt-Ulms G., Klenerman D., Knowles T.P.J., Vendruscolo M, St George-Hyslop P. FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions. Cell, 2018.
  • Ruggeri F.S., Longo G., Castro S., Lipiec E., Pastore A., Dietler G., Infrared Nanospectroscopy characterization of oligomeric and fibrillar aggregates during amyloid formation. Nature Communications, 2015.