Publications

@article{ROTH2024168820,

title = {New aerodynamic lens injector for single particle diffractive imaging},

author = {Nils Roth and Daniel A. Horke and Jannik L\"{u}bke and Amit K. Samanta and Armando D. Estillore and Lena Worbs and Nicolai Pohlman and Kartik Ayyer and Andrew Morgan and Holger Fleckenstein and Martin Domaracky and Benjamin Erk and Christopher Passow and Jonathan Correa and Oleksandr Yefanov and Anton Barty and Sa\v{s}a Bajt and Richard A. Kirian and Henry N. Chapman and Jochen K\"{u}pper},

url = {https://www.sciencedirect.com/science/article/pii/S0168900223008112},

doi = {https://doi.org/10.1016/j.nima.2023.168820},

issn = {0168-9002},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment},

volume = {1058},

pages = {168820},

abstract = {An aerodynamic lens injector was developed specifically for the needs of single-particle diffractive imaging experiments at free-electron lasers. Its design allows for quick changes of injector geometries and focusing properties in order to optimize injection for specific individual samples. Here, we present results of its first use at the FLASH free-electron-laser facility. Recorded diffraction patterns of polystyrene spheres are modeled using Mie scattering, which allowed for the characterization of the particle beam under diffractive-imaging conditions and yielded good agreement with particle-trajectory simulations. The complex refractive index of polystyrene at λ=4.5nm was determined as m=0.976−0.001i.},

keywords = {crystallography, diffractive imaging, experimental design, nanoparticles, Simulation, Single-particle imaging, XFEL},

pubstate = {published},

tppubtype = {article}

}

@article{PhysRevApplied.17.044044,

title = {Optical Funnel to Guide and Focus Virus Particles for X-Ray Diffractive Imaging},

author = {Salah Awel and Sebastian Lavin-Varela and Nils Roth and Daniel A. Horke and Andrei V. Rode and Richard A. Kirian and Jochen K\"{u}pper and Henry N. Chapman},

url = {https://link.aps.org/doi/10.1103/PhysRevApplied.17.044044},

doi = {10.1103/PhysRevApplied.17.044044},

year  = {2022},

date = {2022-04-01},

journal = {Phys. Rev. Applied},

volume = {17},

number = {4},

pages = {044044},

publisher = {American Physical Society},

keywords = {diffractive imaging, nanoparticles},

pubstate = {published},

tppubtype = {article}

}

@article{Zhuang:IUCrJ9:204,

title = {Unsupervised Learning Approaches to Characterizing Heterogeneous Samples Using X-ray Single-Particle Imaging},

author = {Yulong Zhuang and Salah Awel and Anton Barty and Richard Bean and Johan Bielecki and Martin Bergemann and Benedikt J. Daurer and Tomas Ekeberg and Armando D. Estillore and Hans Fangohr and Klaus Giewekemeyer and Mark S. Hunter and Mikhail Karnevskiy and Richard A. Kirian and Henry Kirkwood and Yoonhee Kim and Jayanath Koliyadu and Holger Lange and Romain Letrun and Jannik L\"{u}bke and Abhishek Mall and Thomas Michelat and Andrew J. Morgan and Nils Roth and Amit K. Samanta and Tokushi Sato and Zhou Shen and Marcin Sikorski and Florian Schulz and John C. H. Spence and Patrik Vagovic and Tamme Wollweber and Lena Worbs and P. Lourdu Xavier and Oleksandr Yefanov and Filipe R. N. C. Maia and Daniel A. Horke and Jochen K\"{u}pper and N. Duane Loh and Adrian P. Mancuso and Henry N. Chapman and Kartik Ayyer},

url = {https://scripts.iucr.org/cgi-bin/paper?S2052252521012707},

doi = {10.1107/S2052252521012707},

issn = {2052-2525},

year  = {2022},

date = {2022-03-01},

urldate = {2022-03-14},

journal = {IUCrJ},

volume = {9},

number = {2},

pages = {204--214},

abstract = {One of the outstanding analytical problems in X-ray single-particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and the fact that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. Proposed here are two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA), provides a rough classification which is essentially parameter free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs), can generate 3D structures of the objects at any point in the structural landscape. Both these methods are implemented in combination with the noise-tolerant expand\textendash maximize\textendash compress ( EMC ) algorithm and its utility is demonstrated by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern. Both discrete structural classes and continuous deformations are recovered. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility of moving beyond the study of homogeneous sample sets to addressing open questions on topics such as nanocrystal growth and dynamics, as well as phase transitions which have not been externally triggered.},

keywords = {diffractive imaging, nanoparticles, Single-particle imaging, XFEL},

pubstate = {published},

tppubtype = {article}

}

@article{Lubke:J.Phys.Chem.C125:25794,

title = {Charge-State Distribution of Aerosolized Nanoparticles},

author = {Jannik L\"{u}bke and Nils Roth and Lena Worbs and Daniel A. Horke and Armando D. Estillore and Amit K. Samanta and Jochen K\"{u}pper},

url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.1c06912},

doi = {10.1021/acs.jpcc.1c06912},

issn = {1932-7447, 1932-7455},

year  = {2021},

date = {2021-11-01},

urldate = {2022-01-03},

journal = {J. Phys. Chem. C},

volume = {125},

number = {46},

pages = {25794--25798},

abstract = {In single-particle imaging experiments, beams of individual nanoparticles are exposed to intense pulses of X-rays from free-electron lasers to record diffraction patterns of single, isolated molecules. The reconstruction for structure determination relies on signals from many identical particles. Therefore, well-defined-sample delivery conditions are desired in order to achieve sample uniformity, including avoidance of charge polydispersity. We have observed charging of 220 nm polystyrene particles in an aerosol beam created by a gas-dynamic virtual nozzle focusing technique, without intentional charging of the nanoparticles. Here, we present a deflection method for detecting and characterizing the charge states of a beam of aerosolized nanoparticles. Our analysis of the observed charge-state distribution using optical light-sheet localization microscopy and quantitative particle trajectory simulations is consistent with previous descriptions of skewed charging probabilities of triboelectrically charged nanoparticles.},

keywords = {nanoparticles, Single-particle imaging},

pubstate = {published},

tppubtype = {article}

}

@article{Ayyer:Optica8:15,

title = {3D Diffractive Imaging of Nanoparticle Ensembles Using an X-Ray Laser},

author = {Kartik Ayyer and P. Lourdu Xavier and Johan Bielecki and Zhou Shen and Benedikt J. Daurer and Amit K. Samanta and Salah Awel and Richard Bean and Anton Barty and Martin Bergemann and Tomas Ekeberg and Armando D. Estillore and Hans Fangohr and Klaus Giewekemeyer and Mark S. Hunter and Mikhail Karnevskiy and Richard A. Kirian and Henry Kirkwood and Yoonhee Kim and Jayanath Koliyadu and Holger Lange and Romain Letrun and Jannik L\"{u}bke and Thomas Michelat and Andrew J. Morgan and Nils Roth and Tokushi Sato and Marcin Sikorski and Florian Schulz and John C. H. Spence and Patrik Vagovic and Tamme Wollweber and Lena Worbs and Oleksandr Yefanov and Yulong Zhuang and Filipe R. N. C. Maia and Daniel A. Horke and Jochen K\"{u}pper and N. Duane Loh and Adrian P. Mancuso and Henry N. Chapman},

url = {https://www.osapublishing.org/abstract.cfm?URI=optica-8-1-15},

doi = {10.1364/OPTICA.410851},

issn = {2334-2536},

year  = {2021},

date = {2021-01-01},

urldate = {2021-06-21},

journal = {Optica},

volume = {8},

number = {1},

pages = {15},

keywords = {diffractive imaging, nanoparticles, Single-particle imaging, XFEL},

pubstate = {published},

tppubtype = {article}

}

@article{Sobolev:CommunPhys3:97,

title = {Megahertz Single-Particle Imaging at the European XFEL},

author = {Egor Sobolev and Sergei Zolotarev and Klaus Giewekemeyer and Johan Bielecki and Kenta Okamoto and Hemanth K. N. Reddy and Jakob Andreasson and Kartik Ayyer and Imrich Barak and Sadia Bari and Anton Barty and Richard Bean and Sergey Bobkov and Henry N. Chapman and Grzegorz Chojnowski and Benedikt J. Daurer and Katerina D\"{o}rner and Tomas Ekeberg and Leonie Fl\"{u}ckiger and Oxana Galzitskaya and Luca Gelisio and Steffen Hauf and Brenda G. Hogue and Daniel A. Horke and Ahmad Hosseinizadeh and Vyacheslav Ilyin and Chulho Jung and Chan Kim and Yoonhee Kim and Richard A. Kirian and Henry Kirkwood and Olena Kulyk and Jochen K\"{u}pper and Romain Letrun and N. Duane Loh and Kristina Lorenzen and Marc Messerschmidt and Kerstin M\"{u}hlig and Abbas Ourmazd and Natascha Raab and Andrei V. Rode and Max Rose and Adam Round and Takushi Sato and Robin Schubert and Peter Schwander and Jonas A. Sellberg and Marcin Sikorski and Alessandro Silenzi and Changyong Song and John C. H. Spence and Stephan Stern and Jolanta Sztuk-Dambietz and Anthon Teslyuk and Nicusor Timneanu and Martin Trebbin and Charlotte Uetrecht and Britta Weinhausen and Garth J. Williams and P. Lourdu Xavier and Chen Xu and Ivan A. Vartanyants and Victor S. Lamzin and Adrian Mancuso and Filipe R. N. C. Maia},

url = {http://www.nature.com/articles/s42005-020-0362-y},

doi = {10.1038/s42005-020-0362-y},

issn = {2399-3650},

year  = {2020},

date = {2020-12-01},

urldate = {2021-06-21},

journal = {Commun Phys},

volume = {3},

number = {1},

pages = {97},

abstract = {Abstract The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is expected to provide 27,000 pulses per second, over two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The results obtained pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.},

keywords = {diffractive imaging, nanoparticles, Single-particle imaging, XFEL},

pubstate = {published},

tppubtype = {article}

}

@article{Samanta:StructuralDynamics7:024304,

title = {Controlled Beams of Shock-Frozen, Isolated, Biological and Artificial Nanoparticles},

author = {Amit K. Samanta and Muhamed Amin and Armando D. Estillore and Nils Roth and Lena Worbs and Daniel A. Horke and Jochen K\"{u}pper},

url = {https://aca.scitation.org/doi/10.1063/4.0000004},

doi = {10.1063/4.0000004},

year  = {2020},

date = {2020-03-01},

urldate = {2020-07-21},

journal = {Structural Dynamics},

volume = {7},

number = {2},

pages = {024304},

publisher = {American Institute of Physics},

abstract = {X-ray free-electron lasers promise diffractive imaging of single molecules and nanoparticles with atomic spatial resolution. This relies on the averaging of millions of diffraction patterns of identical particles, which should ideally be isolated in the gas phase and preserved in their native structure. Here, we demonstrated that polystyrene nanospheres and Cydia pomonella granulovirus can be transferred into the gas phase, isolated, and very quickly shock-frozen, i.e., cooled to 4,K within microseconds in a helium-buffer-gas cell, much faster than state-of-the-art approaches. Nanoparticle beams emerging from the cell were characterized using particle-localization microscopy with light-sheet illumination, which allowed for the full reconstruction of the particle beams, focused to $\<$100$mu$m$\<$100,$mu$m$\<$math display="inline" overflow="scroll" altimg="eq-00001.gif"$\>$ $\<$mrow$\>$ $\<$mo$\>\&$lt;$\<$/mo$\>$ $\<$mn$\>$100$\<$/mn$\>$ $\<$mo$\>$,$\<$/mo$\>$ $\<$mi$\>mu\<$/mi$\>$ $\<$mi mathvariant="normal"$\>$m$\<$/mi$\>\<$/mrow$\>\<$/math$\>$, as well as for the determination of particle flux and number density. The experimental results were quantitatively reproduced and rationalized through particle-trajectory simulations. We propose an optimized setup with cooling rates for particles of few-nanometers on nanosecond timescales. The produced beams of shock-frozen isolated nanoparticles provide a breakthrough in sample delivery, e.g., for diffractive imaging and microscopy or low-temperature nanoscience.},

keywords = {Control, experimental design, nanoparticles},

pubstate = {published},

tppubtype = {article}

}

@article{Worbs:Opt.Express27:36580,

title = {Light-Sheet Imaging for the Recording of Transverse Absolute Density Distributions of Gas-Phase Particle-Beams from Nanoparticle Injectors},

author = {Lena Worbs and Lena Worbs and Jannik L\"{u}bke and Jannik L\"{u}bke and Jannik L\"{u}bke and Nils Roth and Nils Roth and Amit K. Samanta and Daniel A. Horke and Daniel A. Horke and Daniel A. Horke and Jochen K\"{u}pper and Jochen K\"{u}pper and Jochen K\"{u}pper},

url = {https://www.osapublishing.org/oe/abstract.cfm?uri=oe-27-25-36580},

doi = {10.1364/OE.27.036580},

issn = {1094-4087},

year  = {2019},

date = {2019-12-01},

urldate = {2020-07-21},

journal = {Opt. Express},

volume = {27},

number = {25},

pages = {36580--36586},

publisher = {Optical Society of America},

abstract = {Imaging biological molecules in the gas-phase requires novel sample delivery methods, which generally have to be characterized and optimized to produce high-density particle beams. A non-destructive characterization method of the transverse particle beam profile is presented. It enables the characterization of the particle beam in parallel to the collection of, for instance, x-ray-diffraction patterns. As a rather simple experimental method, it requires the generation of a small laser-light sheet using a cylindrical telescope and a microscope. The working principle of this technique was demonstrated for the characterization of the fluid-dynamic-focusing behavior of 220 nm polystyrene beads as prototypical nanoparticles. The particle flux was determined and the velocity distribution was calibrated using Mie-scattering calculations.},

keywords = {experimental design, nanoparticles, Single-particle imaging},

pubstate = {published},

tppubtype = {article}

}

@article{Roth:JournalofAerosolScience124:17,

title = {Optimizing Aerodynamic Lenses for Single-Particle Imaging},

author = {Nils Roth and Salah Awel and Daniel A. Horke and Jochen K\"{u}pper},

url = {http://www.sciencedirect.com/science/article/pii/S0021850217304652},

doi = {10.1016/j.jaerosci.2018.06.010},

issn = {0021-8502},

year  = {2018},

date = {2018-10-01},

urldate = {2019-01-15},

journal = {Journal of Aerosol Science},

volume = {124},

pages = {17--29},

abstract = {A numerical simulation infrastructure capable of calculating the flow of gas and the trajectories of particles through an aerodynamic lens injector is presented. The simulations increase the fundamental understanding and predict optimized injection geometries and parameters. Our simulation results were compared to previous reports and also validated against experimental data for 500 nm polystyrene spheres from an aerosol-beam-characterization setup. The simulations yielded a detailed understanding of the radial phase-space distribution and highlighted weaknesses of current aerosol injectors for single-particle diffractive imaging. With the aid of these simulations we developed new experimental implementations to overcome current limitations.},

keywords = {experimental design, nanoparticles, Simulation, Single-particle imaging},

pubstate = {published},

tppubtype = {article}

}

@article{Awel:JApplCryst51:133,

title = {Femtosecond X-Ray Diffraction from an Aerosolized Beam of Protein Nanocrystals},

author = {S. Awel and R. A. Kirian and M. O. Wiedorn and K. R. Beyerlein and N. Roth and D. A. Horke and D. Oberth\"{u}r and J. Knoska and V. Mariani and A. Morgan and L. Adriano and A. Tolstikova and P. L. Xavier and O. Yefanov and A. Aquila and A. Barty and S. Roy-Chowdhury and M. S. Hunter and D. James and J. S. Robinson and U. Weierstall and A. V. Rode and S. Bajt and J. K\"{u}pper and H. N. Chapman},

url = {http://scripts.iucr.org/cgi-bin/paper?te5021},

doi = {10.1107/S1600576717018131},

issn = {1600-5767},

year  = {2018},

date = {2018-02-01},

urldate = {2019-01-24},

journal = {J Appl Cryst},

volume = {51},

number = {1},

pages = {133--139},

abstract = {High-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles used in serial diffraction experiments, which allows the injector to be utilized with standard mountings. As compared with liquid-jet injection, the X-ray scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. Such reduction is required for diffraction measurements of small macromolecular nanocrystals and single particles. High particle speeds are achieved, making the approach suitable for use at upcoming high-repetition-rate facilities.},

keywords = {diffractive imaging, nanoparticles, Single-particle imaging, XFEL},

pubstate = {published},

tppubtype = {article}

}

@article{Beyerlein:IUCrJ4:769,

title = {Mix-and-Diffuse Serial Synchrotron Crystallography},

author = {K. R. Beyerlein and D. Dierksmeyer and V. Mariani and M. Kuhn and I. Sarrou and A. Ottaviano and S. Awel and J. Knoska and S. Fuglerud and O. J\"{o}nsson and S. Stern and M. O. Wiedorn and O. Yefanov and L. Adriano and R. Bean and A. Burkhardt and P. Fischer and M. Heymann and D. A. Horke and K. E. J. Jungnickel and E. Kovaleva and O. Lorbeer and M. Metz and J. Meyer and A. Morgan and K. Pande and S. Panneerselvam and C. Seuring and A. Tolstikova and J. Lieske and S. Aplin and M. Roessle and T. A. White and H. N. Chapman and A. Meents and D. Oberthuer},

url = {//scripts.iucr.org/cgi-bin/paper?ec5004},

doi = {10.1107/S2052252517013124},

issn = {2052-2525},

year  = {2017},

date = {2017-11-01},

urldate = {2019-01-24},

journal = {IUCrJ},

volume = {4},

number = {6},

pages = {769--777},

abstract = {Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50hspace0.25ems show clear binding of chitotriose to the enzyme at a high level of detail. The success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.},

keywords = {crystallography, diffractive imaging, nanoparticles},

pubstate = {published},

tppubtype = {article}

}

@article{Horke:JournalofAppliedPhysics121:123106,

title = {Characterizing Gas Flow from Aerosol Particle Injectors},

author = {Daniel A Horke and Nils Roth and Lena Worbs and Jochen K\"{u}pper},

url = {http://aip.scitation.org/doi/10.1063/1.4978914},

doi = {10.1063/1.4978914},

year  = {2017},

date = {2017-03-01},

journal = {Journal of Applied Physics},

volume = {121},

number = {12},

pages = {123106},

keywords = {experimental design, nanoparticles},

pubstate = {published},

tppubtype = {article}

}

@article{Awel:OpticsExpress24:6507,

title = {Visualizing Aerosol-Particle Injection for Diffractive-Imaging Experiments},

author = {Salah Awel and Richard A Kirian and Niko Eckerskorn and Max Wiedorn and Daniel A Horke and Andrei V Rode and Jochen K\"{u}pper and Henry N Chapman},

url = {http://www.osapublishing.org/viewmedia.cfm?uri=oe-24-6-6507\&seq=0\&html=true},

doi = {10.1364/OE.24.006507},

year  = {2016},

date = {2016-03-01},

journal = {Optics Express},

volume = {24},

number = {6},

pages = {6507--6521},

abstract = {Delivering sub-micrometer particles to an intense x-ray focus is a crucial aspect of single-particle diffractive-imaging experiments at x-ray free-electron lasers. Enabling direct visualization of sub-micrometer aerosol particle streams without interfering with the operation of the particle injector can greatly improve the overall efficiency of single-particle imaging experiments by reducing the amount of time and sample consumed during measurements. We have developed in-situ non-destructive imaging diagnostics to aid real-time particle injector optimization and x-ray/particle-beam alignment, based on laser illumination schemes and fast imaging detectors. Our diagnostics are constructed to provide a non-invasive rapid feedback on injector performance during measurements, and have been demonstrated during diffraction measurements at the FLASH free-electron laser.},

keywords = {diffractive imaging, experimental design, nanoparticles},

pubstate = {published},

tppubtype = {article}

}

@article{Kirian:StructuralDynamics2:041717,

title = {Simple Convergent-Nozzle Aerosol Injector for Single-Particle Diffractive Imaging with X-Ray Free-Electron Lasers},

author = {R A Kirian and S Awel and N Eckerskorn and H Fleckenstein and M Wiedorn and L Adriano and S Bajt and M Barthelmess and R Bean and K R Beyerlein and L M G Chavas and M Domaracky and M Heymann and D A Horke and J Knoska and M Metz and A Morgan and D Oberthuer and N Roth and T Sato and P L Xavier and O Yefanov and A V Rode and J Kupper and H N Chapman},

url = {http://scitation.aip.org/content/aca/journal/sdy/2/4/10.1063/1.4922648},

doi = {10.1063/1.4922648},

year  = {2015},

date = {2015-07-01},

journal = {Structural Dynamics},

volume = {2},

number = {4},

pages = {041717},

keywords = {diffractive imaging, experimental design, nanoparticles, Single-particle imaging, XFEL},

pubstate = {published},

tppubtype = {article}

}