Overview

My research focuses on developing electron diffraction methods and instrumentation to study proteins and protein complexes that are difficult to characterize using X-ray crystallography or single-particle cryo-EM.

AI-based structure prediction has made remarkable progress, but experimental methods are still needed to study protein interactions, locate hydrogen atoms, and understand electrostatic charge distributions, therefore method development stays relevant and important.

Electron diffraction provides a complementary approach to addressing these questions. Due to the strong interaction of electrons with matter and their particular sensitivity to hydrogen atoms and electrostatic charge, electron diffraction enables measurement of structural features that are challenging to access via alternative methodologies.

My research combines detector and microscope development, data-collection methods for radiation-sensitive samples, and applications to structural biology.

Dedicated Narrow-Beam Electron Diffraction Facility

A multipurpose JEOL JEM-F200 transmission electron microscope has been configured as a dedicated scanning electron diffraction instrument. A narrow, parallel electron beam with typical diameter of approximately 40 nm scans across the specimen, while a complete diffraction pattern is recorded at each sampling position. This methodology permits data acquisition from individual nanocrystals or selected regions within protein complexes, rather than requiring averaging over extended areas.

Instrument Specifications:

• Illumination: Cold field-emission gun (sFEG) with four condenser lenses, producing a parallel beam down to 20 nm
• Scanning: Complete scan-descan control via Universal Scan Generator, supporting custom scan patterns
• Sample handling: Cryo-stage with JEOL automated insertion and Gatan ELSA cryo-holder
• Detection: CEOS energy filter coupled with an insertable Cheetah (Medipix3) hybrid pixel camera, plus STEM detector
• Detector test bed: Beamline-style hutch located after the camera chamber houses a 2.5-megapixel PSI JUNGFRAU detector with very high dynamic range; facility remains open for testing new PSI and partner detectors, including high-Z sensors (see HiZfEM below)

The facility operates under the Nanodiffraction group at the Laboratory for Multiscale Bioimaging. Collaborative investigations involving samples amenable to this instrumentation are encouraged.

Current Research Program

1. Detector Development for Electron Diffraction

Detector development has been part of my research since my PhD, when I first worked with the Timepix detector. Various hybrid pixel detector systems have been evaluated for electron diffraction applications, including EIGER, JUNGFRAU with CdTe and GaAs sensors, Timepix, and Medipix3 detectors.

I am currently testing high-Z sensors for electron diffraction at 80-200 keV on the F200, with a focus on detector performance under realistic experimental conditions. With a focus on spatial resolution, speed and dynamic range.

2. Hydrogen Atom and Charge Distribution Mapping in Proteins

Electron diffraction is sensitive to hydrogen atoms and electrostatic charge distributions, which can provide important information about protein–ligand interactions. Within the ProtEDinNanoxtals project, FIB-milled protein nanocrystals were used to investigate hydrogen atom positioning in protein-ligand complexes. This research program examines the capacity of electron diffraction to resolve structural details inaccessible via conventional crystallography.

3. Narrow-Beam Diffraction and Machine Learning Integration

In collaboration with graduate students, machine learning methodologies have been developed for classification of narrow-beam diffraction patterns and phase retrieval from single-molecule diffraction data, including the DiffraGAN computational framework. The next step would be to apply these computational methods to experimental diffraction data collected on the F200, particularly from protein complexes.

4. Beam Damage Characterization and Mitigation

Radiation damage represents a primary limitation for structural investigation of biological specimens via electron microscopy. In partnership with Rasmus Ischebeck, instrumentation is being developed to characterize the response of vitrified (biological) materials to electron beam exposure.

This effort encompasses a correlative light–electron microscopy configuration (SPIE 2026) designed to investigate specimen evolution during irradiation, ultimately informing strategies for maximizing data quality prior to significant beam-induced degradation.

Collaborative Research and Specimen Diversity

Approximately fifty percent of published research output originates from collaborative investigations involving specimens resistant to analysis by conventional structural biology methods. A broad range of challenging radio-sensitive targets have been measured in the past, including malaria parasite hemozoin, peptide nanosheets, zeolites, and additional nanocrystalline materials.

I am particularly interested in challenging samples that cannot easily be studied using conventional methods. If you have a sample that might benefit from electron diffraction, please get in touch.

With our team past and present (see below) We develop hardware, automated methods, alignment procedures and software pipelines to answer questions in relation to structural biology, hydrated materials, synthatic molecules and proteins. 

Former students and early-stage researchers (co)-supervised - Since 2022: Senik Matinyan (PhD, NanED) - Amatassalam Ben Meriem (PhD, NanED) - Min Chavelier Kwon (PhD) - Kirsty Paton (PostDoc, HiZfEM) - Sylvan Guggenbuhl (PostDoc) - Radim Skoupý (PostDoc)  

Collaborators: Jan Pieter Abrahams (PSI / University of Basel) - Rasmus Ischebeck (PSI) - PSI detector group, Erik Fröjdh, Dominic Greiffenberg ( PSI) - Valérie Panneels (PSI) - NanED consortium partners

I completed my PhD at Leiden University (2015) under Jan Pieter Abrahams, working on novel detectors and algorithms for electron nano-crystallography. That work introduced the Timepix hybrid pixel detector to electron diffraction, enabling ab initio structure determination of pharmaceutical nanocrystals at room temperature. After a short Intermezzo at the University of Basel as Post-Doc I joined PSI in 2016, where I got tenured in 2021 and have pursued detector development, 3D electron diffraction of proteins and organic compounds, and the narrow-beam diffraction platform described above.

ORCID: https://orcid.org/0000-0001-8216-1868
Google Scholar: https://scholar.google.com/citations?user=e2OgEWsAAAAJ&hl=en&oi=a

1. Matinyan S, Demir B, Filipcik P, Abrahams JP, van Genderen E. Machine learning for classifying narrow-beam electron diffraction data. Acta Cryst. A 79, 360–368 (2023). 
2. Matinyan S, Filipcik P, van Genderen E, Abrahams JP. DiffraGAN: a conditional GAN for phasing single-molecule diffraction data to atomic resolution. Front. Mol. Biosci. 11, 1386963 (2024).
3. Fröjdh E, …, van Genderen E, … Electron detection with CdTe and GaAs sensors using the charge-integrating hybrid pixel detector JUNGFRAU. J. Instrum. 17, C01020 (2022). 
4. Clabbers MTB, Gruene T, van Genderen E, Abrahams JP. Reducing dynamical electron scattering reveals hydrogen atoms. Acta Cryst. A 75, 82–93 (2019). 
5. Gruene T, …, van Genderen E, … Rapid structure determination of microcrystalline molecular compounds using electron diffraction. Angew. Chem. Int. Ed. 57, 16313–16317 (2018). 
6. Tinti G, Fröjdh E, van Genderen E, et al. Electron crystallography with the EIGER detector. IUCrJ 5, 190–199 (2018).
7. van Genderen E, Clabbers MTB, et al. Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector. Acta Cryst. A 72, 236–242 (2016).