arXiv subjects

Saša Bajt

Publications and source records attributed to Saša Bajt.

14 recordsLinked to original sources

arXiv2026

Femtosecond Three-Dimensional Imaging of Single-Protein with Hard X-ray Laser

The extremely intense pulses of X-ray free-electron lasers (XFELs) have enabled imaging of radiation-sensitive samples, such as macromolecular microcrystals, beyond radiation damage limits. These sources have the potential to deliver biomolecular single-particle imaging, similar to cryo-electron microscopy but without the need for cryo-fixation and with temporal resolution from femtoseconds to milliseconds. While this possibility was recognized before XFELs were built, the biological single-particle imaging work-flow has previously only been demonstrated on large virus particles. Based on decades of improvements in X-ray beam focusing, particle delivery, diffraction detection, and advanced analysis, here we demonstrate imaging of a single molecular complex, the giant-hemoglobin erythrocruorin (Ery) with X-ray laser pulses. Two-dimensional classes of diffraction patterns could be reconstructed to 15 Angstrom resolution, and 3D images to approximately 20 Angstrom, while the 3D merged intensity in reciprocal space extended beyond 20 Angstrom. The resolution discrepancy is likely due to heterogeneity caused by gas-phase compaction of the complexes. With increased throughput, this approach could be used to reveal in-situ structural details during mass spectrometry studies of biomolecules, while improvements in sample delivery may provide ultrafast snapshot imaging of biological single-particles in their native-state beyond the limitations of radiation damage.

physics.bio-ph↗

arXiv2026

Convergent-Beam X-ray Crystallography

Molecular and polymeric crystals show a wide range of functional properties that arise from the interplay between the atomic-scale structure of their constituent molecules and the organization of these molecules within the crystal lattice at macroscopic length scales. X-ray diffraction can provide structural information at these disparate length scales, but usually only through experiments that address one or the other of molecular (or unit-cell) structure versus crystal structure. Consequently, the accuracy of determined molecular or polymer structures may be limited by unaccounted crystal inhomogeneities of the crystal lattice and the characterization of crystalline materials might not reveal the underlying causes of crystal morphology. Here we introduce X-ray convergent-beam diffraction to obtain spatially-resolved structural information from crystals by projection topographic imaging. Using highly focusing X-ray multilayer Laue lenses, we show that Bragg reflections can be mapped into tomographic images of the crystal, for the characterization of strain and defects at high resolution. We demonstrate how the crystal morphology obtained this way can be accounted for when determining structure factors as a function of position in the crystal. The approach may assist in studies such as diffusion and binding in MOFS, protein-drug binding, crystal growth, and the mechanical responses of photo-reactive or thermally driven dynamic crystals.

cond-mat.mtrl-sci↗

arXiv2025

Single-particle incoherent diffractive imaging and amplified spontaneous emission in copper nanocubes

We demonstrate element-specific incoherent diffractive imaging (IDI) of single copper nanocubes using intensity correlations of K$α$ fluorescence at a hard X-ray free-electron laser. Combining single particle diffraction classification with IDI, we retrieve the form factor of 88 nm cubes with 20 nm resolution, extending IDI to the destructive single-particle regime with a large gain in resolution. IDI visibility drops sharply above a fluence of $10^2$ J/cm$^2$, consistent with the assumption of amplified spontaneous emission. Our results reveal fundamental limits for high-fluence nanoimaging towards future single-particle X-ray imaging.

physics.optics↗

arXiv2025

Nonlinear phenomena in X-ray fluorescence from single nanoparticles under extreme conditions

Materials exposed to intense femtosecond X-ray pulses with energies above their K-shell absorption edge can enter an extremely ionized state, which could give rise to nonlinear phenomena, such as saturable absorption and reverse saturable absorption. In this work, we investigate these effects on single copper nanoparticles irradiated by an X-ray free-electron laser pulse. We study the properties of the K$α$ fluorescence for two different short pulse durations and three X-ray incident energies below and above the K-shell absorption edge, and correlate these with incident fluence estimates based on coherent diffraction. We observe that the incident fluence of the pulse and not its duration, is the main factor that modulates the nonlinear response, which leads to an effective shortening of the fluorescence emission. Our findings have implications for fluorescence-based methods for imaging single particles using transiently coherent fluorescence, or diffractive imaging through transient resonances.

physics.optics↗

arXiv2024

Convergent-beam attosecond X-ray crystallography

Sub-angstrom spatial resolution of electron density coupled with sub-femtosecond temporal resolution is required to directly observe the dynamics of the electronic structure of a molecule after photoinitiation or some other ultrafast perturbation. Meeting this challenge, pushing the field of quantum crystallography to attosecond timescales, would bring insights into how the electronic and nuclear degrees of freedom couple, enable the study of quantum coherences involved in molecular dynamics, and ultimately enable these dynamics to be controlled. Here we propose to reach this realm by employing convergent-beam X-ray crystallography with high-power attosecond pulses from a hard-X-ray free-electron laser. We show that with dispersive optics, such as multilayer Laue lenses of high numerical aperture, it becomes possible to encode time into the resulting diffraction pattern with deep sub-femtosecond precision. Each snapshot diffraction pattern consists of Bragg streaks that can be mapped back to arrival times and positions of X-rays on the face of a crystal. This can span tens of femtoseconds, and can be finely sampled as we demonstrate experimentally. The approach brings several other advantages, such as an increase of the number of observable reflections in a snapshot diffraction pattern, all fully integrated, to improve the speed and accuracy of serial crystallography -- especially for crystals of small molecules.

physics.optics↗

arXiv2022

On the use of multilayer Laue lenses with X-ray Free Electron Lasers

Multilayer Laue lenses were used for the first time to focus x-rays from an X-ray Free Electron Laser (XFEL). In an experiment, which was performed at the European XFEL, we demonstrated focusing to a spot size of a few tens of nanometers. A series of runs in which the number of pulses per train was increased from 1 to 2, 3, 4, 5, 6, 7, 10, 20 and 30 pulses per train, all with a pulse separation of 3.55 us, was done using the same set of lenses. The increase in the number of pulses per train was accompanied with an increase of x-ray intensity (transmission) from 9% to 92% at 5 pulses per train, and then the transmission was reduced to 23.5 % when the pulses were increased further. The final working condition was 30 pulses per train and 23.5% transmission. Only at this condition we saw that the diffraction efficiency of the MLLs changed over the course of a pulse train, and this variation was reproducible from train to train. We present the procedure to align and characterize these lenses and discuss challenges working with the pulse trains from this unique x-ray source.

physics.acc-ph↗

arXiv2020

New aerodynamic lens injector for single particle diffractive imaging

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 yield good agreement with particle-trajectory simulations.

physics.ins-det↗

arXiv2020

A ray-trace analysis of X-ray multilayer Laue lenses for nanometer focusing

Thick diffractive optical elements offer a promising way to achieve focusing or imaging at a resolution approaching 1 nm for X-ray wavelengths shorter than about 0.1 nm. Efficient focusing requires that these are fabricated with structures that vary in period and orientation so that rays obey Bragg's law over the entire lens aperture and give rise to constructive interference at the focus. Here the analysis method of ray-tracing of thick diffractive optical elements is applied to such lenses to optimise their designs and to investigate their operating and manufacturing tolerances. Expressions are provided of the fourth-order series expansions of the wavefront aberrations and transmissions of both axi-symmetric lenses and pairs of crossed lenses that each focuses in only one dimension like a cylindrical lens. We find that aplanatic zone-plate designs, whereby aberrations are corrected over a large field of view, can be achieved by axi-symmetric lenses but not the crossed lenses. We investigate the performance of 1 nm-resolution lenses with focal lengths of about 1 mm and show their fields of view are mainly limited by the acceptance angle of Bragg diffraction, and that aberrations can limit the performance of lenses with longer focal lengths. We apply the ray-tracing formalism for a tolerancing analysis of imperfect lenses and examine some strategies for the correction of their aberrations.

physics.optics↗

arXiv2020

Ptychographic X-ray Speckle Tracking

We present a method for the measurement of the phase gradient of a wavefront by tracking the relative motion of speckles in projection holograms as a sample is scanned across the wavefront. By removing the need to obtain an un-distorted reference image of the sample, this method is suitable for the metrology of highly divergent wavefields. Such wavefields allow for large magnification factors, that, according to current imaging capabilities, will allow for nano-radian angular sensitivity and nano-scale sample projection imaging. Both the reconstruction algorithm and the imaging geometry are nearly identical to that of ptychography, except that the sample is placed downstream of the beam focus and that no coherent propagation is explicitly accounted for. Like other x-ray speckle tracking methods, it is robust to low-coherence x-ray sources making is suitable for lab based x-ray sources. Likewise it is robust to errors in the registered sample positions making it suitable for x-ray free-electron laser facilities, where beam pointing fluctuations can be problematic for wavefront metrology. We also present a modified form of the speckle tracking approximation, based on a second-order local expansion of the Fresnel integral. This result extends the validity of the speckle tracking approximation and may be useful for similar approaches in the field.

physics.optics↗

arXiv2020

Ptychographic X-ray Speckle Tracking with Multi Layer Laue Lens Systems

The ever-increasing brightness of synchrotron radiation sources demands improved x-ray optics to utilise their capability for imaging and probing biological cells, nano-devices, and functional matter on the nanometre scale with chemical sensitivity. Hard x-rays are ideal for high-resolution imaging and spectroscopic applications due to their short wavelength, high penetrating power, and chemical sensitivity. The penetrating power that makes x-rays useful for imaging also makes focusing them technologically challenging. Recent developments in layer deposition techniques that have enabled the fabrication of a series of highly focusing x-ray lenses, known as wedged multi layer Laue lenses. Improvements to the lens design and fabrication technique demands an accurate, robust, in-situ and at-wavelength characterisation method. To this end, we have developed a modified form of the speckle-tracking wavefront metrology method, the ptychographic x-ray speckle tracking method, which is capable of operating with highly divergent wavefields. A useful by-product of this method, is that it also provides high-resolution and aberration-free projection images of extended specimens. We report on three separate experiments using this method, where we have resolved ray path angles to within 4 nano-radians with an imaging resolution of 45nm (full-period). This method does not require a high degree of coherence, making it suitable for lab based x-ray sources. Likewise it is robust to errors in the registered sample positions making it suitable for x-ray free-electron laser facilities, where beam pointing fluctuations can be problematic for wavefront metrology.

physics.optics↗

arXiv2020

speckle-tracking: a Software Suite for Ptychographic X-ray Speckle Tracking

In recent years, x-ray speckle tracking techniques have emerged as viable tools for wavefront metrology and sample imaging applications. These methods are based on the measurement of near-field images. Thanks to the simple experimental set-up, high angular sensitivity and compatibility with low coherence sources these methods have been actively developed for use with synchrotron and laboratory light sources. Not only do speckle-tracking techniques give the potential for high resolution imaging, but they also provide rapid and robust characterisation of aberrations of x-ray optical elements, focal spot profiles and the sample position and transmission properties. In order to realise these capabilities, we require software implementations that are equally rapid and robust. To address this need, a software suite has been developed for the "ptychographic x-ray speckle tracking technique" -- an x-ray speckle based method suitable for highly divergent wavefields. The software suite is written in Python 3, with an OpenCL back end for GPU and multi-CPU core processing. It is accessible as a Python module, through the command line or through a graphical user interface and is available as source code under version 3 or later of the GNU General Public License.

eess.IV↗

arXiv2018

Femtosecond x-ray diffraction from an aerosolized beam of protein nanocrystals

We demonstrate near-atomic-resolution Bragg diffraction from aerosolized single granulovirus crystals using an x-ray free-electron laser. The form of the aerosol injector is nearly identical to conventional liquid-microjet nozzles, but the x-ray-scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. This approach provides a route to study the weak diffuse or lattice-transform signal arising from small crystals. The high speed of the particles is particularly well suited to upcoming MHz-repetition-rate x-ray free-electron lasers.

physics.bio-ph↗

arXiv2014

Spin precession mapping at ferromagnetic resonance via nuclear resonant scattering

We probe the spin dynamics in a thin magnetic film at ferromagnetic resonance by nuclear resonant scattering of synchrotron radiation at the 14.4 keV resonance of $^{57}$Fe. The precession of the magnetization leads to an apparent reduction of the magnetic hyperfine field acting at the $^{57}$Fe nuclei. The spin dynamics is described in a stochastic relaxation model adapted to the ferromagnetic resonance theory by Smit and Beljers to model the decay of the excited nuclear state. From the fits of the measured data the shape of the precession cone of the spins is determined. Our results open a new perspective to determine magnetization dynamics in layered structures with very high depth resolution by employing ultrathin isotopic probe layers.

cond-mat.mtrl-sci↗

arXiv2014

X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser

We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e. g., structural-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules.

physics.atom-ph↗