Controlling the Motion of Complex Molecules and Particles (COMOTION)

Recent advances in X-ray free-electron laser have enabled the observation of near-atomic-resolution structures in diffraction before-destruction experiments, for instance, of isolated mimiviruses and of proteins from microscopic crystals. The goal to record molecular movies with spatial and temporal atomic-resolution (femtoseconds and picometers) on individual molecules is near. Furthermore, the investigation of ultrafast, sub-femtosecond electron dynamics in small molecules is providing first results. Its extension to large molecules promises the unraveling of charge migration and energy transport in complex (bio)molecular systems. Novel matter-wave experiments with large molecules are testing the limits of quantum mechanics, particle-wave duality, and coherence. Extending these metrology experiments to larger systems will widen our understanding of the underlying physics whilst also allowing the precise measurement of molecular properties.

The principal obstacle for these and similar experiments across the molecular sciences is the controlled production of identical samples of individual molecules in the gas phase

Within the COMOTION project we focus our research efforts on

Cold and controlled large molecules

Efforts on creating controlled samples for ideal single-particle-diffraction experiments: High-density, shockfrozen, laser-aligned native-structure samples of biological macromolecules

Optically Controlled Particles

Approaches for the production of purified high-density beams of a broad variety of biological nanoparticles and establish control through electric fields and optical fields from a laser.

Freeze-and-deposit sample delivery

Development of a novel, disruptive sample-preparation approach for cryo-electron microscopy

Diffractive Imaging

Imaging and reconstruction of the three-dimensional molecular structure of isolated (biological) molecules and nanoparticles at atomic resolution.

Novel molecule sources

Methodologies to vaporise large (bio)molecules and particles and efficiently inject them into vacuum for further manipulation.

Most relevant funding

Funded through an ERC Consolidator Grant (ERC-CoG 614507-COMOTION)

Publications

Recent preprints

Amin, M. ; Hartmann, J.-M. ; Samanta, A. K. ; Küpper, J. (Corresponding author)
Laser-induced alignment of nanoparticles and macromolecules for single-particle-imaging applications
[10.3204/PUBDB-2024-01943] OpenAccess Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Hoeing, D. ; Salzwedel, R. ; Worbs, L. ; Zhuang, Y. ; Samanta, A. K. ; Lübke, J. ; Estillore, A. D. ; Dlugolecki, K. ; Passow, C. ; Erk, B. ; Ekanayake, N. ; Ramm, D. ; Correa, J. ; Papadopoulou, C. C. ; Noor, A. T. ; Schulz, F. ; Selig, M. ; Knorr, A. (Corresponding author) ; Ayyer, K. (Corresponding author) ; Küpper, J. (Corresponding author) ; Lange, H. (Corresponding author)
Time-Resolved Single-Particle X-ray Scattering Reveals Electron-Density Gradients As Coherent Plasmonic-Nanoparticle-Oscillation Source
arXiv Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Ekeberg, T. ; Assalauova, D. ; Bielecki, J. ; Boll, R. ; Daurer, B. J. ; Eichacker, L. A. ; Franken, L. E. ; Galli, D. E. ; Gelisio, L. ; Gumprecht, L. ; Gunn, L. H. ; Hajdu, J. ; Hartmann, R. ; Hasse, D. ; Ignatenko, A. ; Koliyadu, J. ; Kulyk, O. ; Kurta, R. ; Kuster, M. ; Lugmayr, W. ; Lübke, J. ; Mancuso, A. P. ; Mazza, T. ; Nettelblad, C. ; Ovcharenko, Y. ; Rivas, D. E. ; Samanta, A. K. ; Schmidt, P. ; Sobolev, E. ; Timneanu, N. ; Usenko, S. ; Westphal, D. ; Wollweber, T. ; Worbs, L. ; Xavier, P. L. ; Yousef, H. ; Ayyer, K. ; Chapman, H. N. ; Sellberg, J. A. ; Seuring, C. ; Vartanyants, I. A. ; Küpper, J. ; Meyer, M. ; Maia, F. R. N. C. (Corresponding author)
Observation of a single protein by ultrafast X-ray diffraction
[10.1101/2022.03.09.483477] OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Roth, N. ; Horke, D. A. ; Lübke, J. ; Samanta, A. K. (Corresponding author) ; Estillore, A. D. ; Worbs, L. ; Pohlman, N. ; Ayyer, K. ; Morgan, A. ; Fleckenstein, H. ; Domaracky, M. ; Erk, B. ; Passow, C. ; Correa, J. ; Yefanov, O. ; Barty, A. ; Bajt, S. ; Kirian, R. ; Chapman, H. N. ; Küpper, J. (Corresponding author)
New aerodynamic lens injector for single particle diffractive imaging
arXiv Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Mullins, T. ; Karamatskos, E. T. ; Wiese, J. ; Onvlee, J. ; Rouzée, A. ; Yachmenev, A. ; Trippel, S. ; Küpper, J. (Corresponding author)
Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules
arXiv Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Peer-reviewed publications

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Breakthrough in laser-alignment for macromolecular single-particle imaging

10 April 2025

Single-particle diffractive imaging (SPI) using X-ray free-electron lasers allows researchers to reconstruct the structure of nanoparticles and biomolecules. However, the technique often requires imaging up to several billion nanoparticles to produce the image and imposes limitations on its clarity and sharpness. Researchers at the Center for Free-Electron Laser Science at DESY, together with international colleagues, recently demonstrated that laser-induced alignment can indeed be achieved to significantly improve molecular imaging techniques. This geometric confinement of the molecules in the x-ray-imaging experiment will greatly facilitate the recovery of the molecular orientation and, therefore, the structure retrieval. It thus overcomes a significant challenge in single-particle diffractive imaging. This novel development further paves the way for solving the three-dimensional structures of proteins and other macromolecules using SPI.

Timepix3: single-pixel multi-hit energy-measurement behaviour

13 November 2024

The event-driven hybrid-pixel detector readout chip, Timepix3, has the ability to simultaneously measure the time of an event on the nanosecond timescale and the energy deposited in the sensor. However, the behaviour of the system when two events are recorded in quick succession of each other on the same pixel was not studied in detail previously. We present experimental measurements, circuit simulations, and an empirical model for the impact of a preceding event on this energy measurements, which can result in a loss as high as 70%. Accounting for this effect enables more precise compensation, particularly for phenomena like timewalk. This results in significant improvements in time resolution — in the best case, multiple tens of nanoseconds — when two events happen in rapid succession.

Recent Publications

Journal Article Peravali, S. K. (Corresponding author)CFEL*Extern* ; Samanta, A. K.CFEL*XFEL.EU*DESY* ; Amin, M.CFEL*Extern* ; Neumann, P.Extern*DESY* ; Küpper, J.CFEL*XFEL.EU*DESY* ; Breuer, M. (Corresponding author)CFEL*
An improved numerical simulation methodology for nanoparticle injection through aerodynamic lens systems
Physics of fluids 37, 033380 (2025) [10.1063/5.0260295]2025 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Amin, M.CFEL*Extern* ; Hartmann, J.-M. ; Samanta, A. K.CFEL*XFEL.EU*DESY* ; Küpper, J. (Corresponding author)CFEL*XFEL.EU*DESY*
Laser-induced alignment of nanoparticles and macromolecules for single-particle-imaging applications
Journal of the American Chemical Society 147(9), 7445 - 7451 (2025) [10.1021/jacs.4c15679]2025 Embargoed OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article He, L.CFEL*Extern*XFEL.EU* ; Johny, M.CFEL*Extern*XFEL.EU* ; Kierspel, T.CSSB*DESY* ; Dlugolecki, K.CFEL*XFEL.EU*DESY* ; Bari, S.DESY* ; Boll, R.XFEL.EU* ; Bromberger, H.CFEL*XFEL.EU*DESY* ; coreno, m.Extern*XFEL.EU* ; De Fanis, A.XFEL.EU* ; Di Fraia, M.Extern* ; Erk, B.XFEL.EU*DESY* ; Gisselbrecht, M.Extern* ; Grychtol, P.XFEL.EU* ; Eng-Johnsson, P.Extern*XFEL.EU* ; Mazza, T.XFEL.EU* ; Onvlee, J.CFEL*Extern*XFEL.EU* ; Ovcharenko, Y.XFEL.EU* ; Petrovic, J.Extern*XFEL.EU*DESY* ; Rennhack, N.XFEL.EU* ; Rivas, D.XFEL.EU* ; Rudenko, A.Extern* ; Ruehl, E.Extern* ; Schwob, L.XFEL.EU*DESY* ; Simon, M.Extern* ; Trinter, F.Extern*XFEL.EU* ; Usenko, S.XFEL.EU* ; Wiese, J.CFEL*Extern*XFEL.EU* ; Meyer, M.XFEL.EU* ; Trippel, S. (Corresponding author)CFEL*XFEL.EU*DESY* ; Küpper, J. (Corresponding author)CFEL*XFEL.EU*DESY*
Controlled molecule injector for cold, dense, and pure molecular beams at the European x-ray free-electron laser
Review of scientific instruments 95(11), 113301 (2024) [10.1063/5.0219086]2024 OpenAccess Files Fulltext BibTeX | EndNote: XML, Text | RIS