arXiv subjects

Johan Bielecki

Publications and source records attributed to Johan Bielecki.

At least 19 recordsLinked to original sources

arXiv2026

Train-Resolved Statistical Recovery of Weak SAXS Signals in Liquids at the European XFEL

We present a train-resolved SAXS methodology for recovering weak scattering signals from high-repetition-rate XFEL datasets and apply it to aqueous L-cysteine solutions measured at the European XFEL. Independent scale-plus-offset fitting was performed for matched cysteine and water train pairs, followed by subtraction of transmission-matched water--water controls. The 0.5 M dataset reveals a reproducible sign-changing residual SAXS signal that increases with incident XFEL transmission and remains after removal of detector-wide scaling, additive offsets, and matched water--water control residuals. Convergence and block-averaging analyses show that the residual emerges progressively as independent train pairs are accumulated and exhibits uncertainty scaling close to the expected inverse square-root dependence on N. These results establish a statistically robust transmission-dependent residual SAXS contribution whose microscopic origin remains unresolved, while demonstrating that train-resolved observables combined with matched controls can substantially improve sensitivity to weak scattering signals in high-repetition-rate XFEL experiments.

physics.optics↗

arXiv2026

Imaging aerosolized viruses with an X-ray free-electron laser using single-particle rotational invariants

X-ray free-electron lasers (XFELs) enable diffraction-before-destruction measurements of individual nanosized bioparticles, making it possible to study the structure and dynamics of non-crystalline targets under near-biologically relevant conditions. In this work, we employ rotational invariants for model-guided and ab initio three-dimensional (3D) structure determination of aerosolized bacteriophages PR772 measured with an XFEL. The rotational invariants derived from diffraction patterns collected during multiple independent XFEL experiments facilitate the characterization of similarities and structural variations within the measured ensembles of PR772 particles. Despite modest experimental resolution, we can identify various structural features of the viruses, including the asymmetric nature of capsid distortions from the perfect icosahedral shape, density variations in the encapsulated content, and an extension at one of the capsid vertices. Rotational invariants combine structural sensitivity with applicability to forward-scattering modeling and inverse problem solving, making them powerful tools for probing the structure and temporal evolution of nano- and bioparticles using an XFEL, particularly enhancing the fidelity of structural analysis at limited experimental resolution.

physics.bio-ph↗

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↗

arXiv2025

Single-Particle X-ray Scattering Reveals a High Local Supersaturation of Precursors as the Origin of CoO Assembly Formation

Single-particle small-angle X-ray scattering (SP-SAXS) enables quantitative morphological analysis by recording diffraction snapshots from isolated particles using X-ray free-electron laser (XFEL) pulses. Unlike conventional X-ray techniques, which average over the entire illuminated sample volume, SP-SAXS resolves low-contrast, less abundant, or transient species within heterogeneous particle populations that would otherwise remain hidden. Here, we apply SP-SAXS to investigate the solvothermal formation of CoO nanocrystal assemblies from a Co(acac)$_3$ precursor in benzyl alcohol. The single-particle data reveal amorphous, uniform-density Co(acac)$_2$ spheres as transient intermediates that directly crystallize into cavernous CoO nanocrystal assemblies, which explains why CoO forms as hierarchical aggregates rather than as isolated nanocrystals. These results demonstrate that SP-SAXS provides a powerful framework for disentangling morphological heterogeneity in nanoparticle formation processes.

cond-mat.mes-hall↗

arXiv2025

Dichography: Two-frame Ultrafast Imaging from a Single Diffraction Pattern

We experimentally demonstrate that pairs of time-delayed ultrabright and ultrashort X-ray pulses of two different colors, delivered by modern X-ray Free Electron Lasers, can provide two time-delayed snapshots of a sample. We introduce Dichography, a method that algorithmically separates the diffraction signals overlapping on the detector and independently retrieves the two images of the specimen. We employ Dichography to reconstruct two views of individual xenon-doped helium nanodroplets with 20 nm spatial resolution. The consistency of structures observed in both images at delays up to 750 fs provides evidence that, under these illumination conditions, significant structural damage only occurs at longer timescales. We further validate the method by imaging pairs of silver nanoparticles intercepted by the same light pulse. Dichography enables a new class of experiments across physics, chemistry, and materials science, making a significant step toward the original promise of X-ray free-electron lasers to capture ultrafast movies of nanomatter.

physics.optics↗

arXiv2025

Direct observation of the exciton polaron by serial femtosecond crystallography on single CsPbBr$_3$ quantum dots

The outstanding opto-electronic properties of lead halide perovskites have been related to the formation of polarons. Nevertheless, the observation of the atomistic deformation brought about by one electron-hole pair in these materials has remained elusive. Here, we measure the diffraction patterns of single CsPbBr$_3$ quantum dots (QDs) with and without resonant excitation in the single exciton limit using serial femtosecond crystallography (SFX). By reconstructing the 3D differential diffraction pattern, we observe small shifts of the Bragg peaks indicative of a crystal-wide deformation field. Building on DFT calculations, we show that these shifts are consistent with the lattice distortion induced by a delocalized electron and a localized hole, forming a mixed large/small exciton polaron. This result creates a clear picture of the polaronic deformation in CsPbBr$_3$ QDs, highlights the exceptional sensitivity of SFX to lattice distortions in few-nanometer crystallites, and establishes an experimental platform for future studies of electron-lattice interactions.

cond-mat.mtrl-sci↗

arXiv2024

Impact of gas background on XFEL single-particle imaging

Single-particle imaging (SPI) using X-ray free-electron Lasers (XFELs) offers the potential to determine protein structures at high spatial and temporal resolutions without the need for crystallization or vitrification. However, the technique faces challenges due to weak diffraction signals from single proteins and significant background scattering from gases used for sample delivery. A recent observation of a diffraction pattern from an isolated GroEL protein complex had similar numbers of signal and background photons. Ongoing efforts aim to reduce the background created by sample delivery, with one approach replacing most of the used gas with helium. In this study, we investigate the effects of a potentially reduced background on the resolution limits for SPI of isolated proteins under different experiment conditions. As a test case, we used GroEL, and we used experimentally measured parameters for our simulations. We observe that background significantly impacts the achievable resolution, particularly when the signal strength is comparable to the background, and a background reduction would lead to a significant improvement in resolution.

q-bio.BM↗

arXiv2024

Observation of Aerosolization-induced Morphological Changes in Viral Capsids

Single-stranded RNA viruses co-assemble their capsid with the genome and variations in capsid structures can have significant functional relevance. In particular, viruses need to respond to a dehydrating environment to prevent genomic degradation and remain active upon rehydration. Theoretical work has predicted low-energy buckling transitions in icosahedral capsids which could protect the virus from further dehydration. However, there has been no direct experimental evidence, nor molecular mechanism, for such behaviour. Here we observe this transition using X-ray single particle imaging of MS2 bacteriophages after aerosolization. Using a combination of machine learning tools, we classify hundreds of thousands of single particle diffraction patterns to learn the structural landscape of the capsid morphology as a function of time spent in the aerosol phase. We found a previously unreported compact conformation as well as intermediate structures which suggest an incoherent buckling transition which does not preserve icosahedral symmetry. Finally, we propose a mechanism of this buckling, where a single 19-residue loop is destabilised, leading to the large observed morphology change. Our results provide experimental evidence for a mechanism by which viral capsids protect themselves from dehydration. In the process, these findings also demonstrate the power of single particle X-ray imaging and machine learning methods in studying biomolecular structural dynamics.

q-bio.BM↗

arXiv2024

Resolving non-equilibrium shape variations amongst millions of gold nanoparticles

Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with x-ray free-electron lasers (XFELs) creates unprecedented opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between $10^5$ structural models and $10^6$ XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the non-equilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable `shape envelope' amongst nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles' shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.

cond-mat.mes-hall↗

arXiv2023

Helium-Electrospray: an improved sample delivery system for single-particle imaging with X-ray lasers

Imaging the structure and observing the dynamics of isolated proteins using single-particle X-ray diffractive imaging (SPI) is one of the potential applications of X-ray free-electron lasers (XFELs). Currently, SPI experiments on isolated proteins are limited by three factors: low signal strength, limited data and high background from gas scattering. The last two factors are largely due to the shortcomings of the aerosol sample delivery methods in use. Here we present our modified electrospray ionization (ESI) source, which we dubbed Helium-ESI (He-ESI). With it, we increased particle delivery into the interaction region by a factor of 10, for 26 nm-sized biological particles, and decreased the gas load in the interaction chamber corresponding to an 80% reduction in gas scattering when compared to the original ESI. These improvements will lead to a significant increase in the quality and quantity of SPI diffraction patterns in future experiments using He-ESI, resulting in higher-resolution structures.

physics.ins-det↗

arXiv2023

3D-Printed Sheet Jet for Stable Megahertz Liquid Sample Delivery at X-ray Free Electron Lasers

X-ray Free Electron Lasers (XFELs) can probe chemical and biological reactions as they unfold with unprecedented spatial and temporal resolution. A principal challenge in this pursuit is the delivery of samples to the X-ray interaction point in a way that produces data of the highest possible quality and efficiency. This is hampered by constraints posed by the light source and operation within a beamline environment. For liquid samples, the solution typically involves a high-speed liquid jet, capable of keeping up with the rate of X-ray pulses. However, conventional jets are not ideal because of radiation-induced explosions of the jet, as well as their cylindrical geometry combined with the X-ray pointing instability of many beamlines causes the interaction volume to differ for every pulse. This complicates data analysis and contributes to measurement errors. An alternative geometry is a liquid sheet jet which, with its constant thickness over large areas, eliminates the X-ray pointing related problems. Since liquid sheets can be made very thin, the radiation-induced explosion is reduced, boosting their stability. They are especially attractive for experiments which benefit from small interaction volumes such as fluctuation X-ray scattering and several types of spectroscopy. Although they have seen increasing use for soft X-ray applications in recent years, there has not yet been wide-scale adoption at XFELs. Here, we demonstrate liquid sheet jet sample injection at the European XFEL. We evaluate several aspects of its performance relative to a conventional liquid jet including thickness profile, stability, and radiation-induced explosion dynamics at high repetition rates. The sheet jet exhibits superior performance across these critical experimental parameters. Its minute thickness also suggests ultrafast single-particle solution scattering is a possibility.

physics.ins-det↗

arXiv2021

Unsupervised learning approaches to characterize heterogeneous samples using X-ray single particle imaging

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 that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. We propose 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. We implement both these methods in combination with the noise-tolerant expand-maximize-compress (EMC) algorithm and demonstrate its utility by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern and recover both discrete structural classes as well as continuous deformations. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility to move beyond studying homogeneous sample sets and study open questions on topics such as nanocrystal growth and dynamics as well as phase transitions which have not been externally triggered.

eess.IV↗

arXiv2020

Ptychographic wavefront characterisation for single-particle imaging at X-ray lasers

A well-characterised wavefront is important for many X-ray free-electron laser (XFEL) experiments, especially for single-particle imaging (SPI), where individual bio-molecules randomly sample a nanometer-region of highly-focused femtosecond pulses. We demonstrate high-resolution multiple-plane wavefront imaging of an ensemble of XFEL pulses, focused by Kirkpatrick-Baez (KB) mirrors, based on mixed-state ptychography, an approach letting us infer and reduce experimental sources of instability. From the recovered wavefront profiles, we show that while local photon fluence correction is crucial and possible for SPI, a small diversity of phase-tilts likely has no impact. Our detailed characterisation will aid interpretation of data from past and future SPI experiments, and provides a basis for further improvements to experimental design and reconstruction algorithms.

physics.optics↗

arXiv2020

3D diffractive imaging of nanoparticle ensembles using an X-ray laser

We report the 3D structure determination of gold nanoparticles (AuNPs) by X-ray single particle imaging (SPI). Around 10 million diffraction patterns from gold nanoparticles were measured in less than 100 hours of beam time, more than 100 times the amount of data in any single prior SPI experiment, using the new capabilities of the European X-ray free electron laser which allow measurements of 1500 frames per second. A classification and structural sorting method was developed to disentangle the heterogeneity of the particles and to obtain a resolution of better than 3 nm. With these new experimental and analytical developments, we have entered a new era for the SPI method and the path towards close-to-atomic resolution imaging of biomolecules is apparent.

physics.app-ph↗

arXiv2019

Megahertz single-particle imaging at the European XFEL

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 will soon provide 27,000 pulses per second, more than 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 obtained results pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

physics.ins-det↗

arXiv2017

Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles

Ultrafast X-ray imaging provides high resolution information on individual fragile specimens such as aerosols, metastable particles, superfluid quantum systems and live biospecimen, which is inaccessible with conventional imaging techniques. Coherent X-ray diffractive imaging, however, suffers from intrinsic loss of phase, and therefore structure recovery is often complicated and not always uniquely-defined. Here, we introduce the method of in-flight holography, where we use nanoclusters as reference X-ray scatterers in order to encode relative phase information into diffraction patterns of a virus. The resulting hologram contains an unambiguous three-dimensional map of a virus and two nanoclusters with the highest lat- eral resolution so far achieved via single shot X-ray holography. Our approach unlocks the benefits of holography for ultrafast X-ray imaging of nanoscale, non-periodic systems and paves the way to direct observation of complex electron dynamics down to the attosecond time scale.

physics.atm-clus↗

arXiv2015

Short-Range Structure and Phonon Assignment of the Brownmillerite-Type Oxide Ba$_{2}$In$_{2}$O$_{5}$ and its Hydrated Proton-Conducting Form BaInO$_{3}$H

The vibrational spectra and short-range structure of the brownmillerite-type oxide Ba$_{2}$In$_{2}$O$_{5}$ and its hydrated form BaInO$_{3}$H, are investigated by means of Raman, infrared, and inelastic neutron scattering spectroscopies together with density functional theory calculations. For Ba$_{2}$In$_{2}$O$_{5}$, which may be described as an oxygen deficient perovskite structure with alternating layers of InO$_{6}$ octahedra and InO$_{4}$ tetrahedra, the results affirm a short-range structure of $Icmm$ symmetry, which is characterized by random orientation of successive layers of InO$_{4}$ tetrahedra. For the hydrated, proton conducting, form, BaInO$_{3}$H, the results suggest that the short-range structure is more complicated than the $P4/mbm$ symmetry that has been proposed previously on the basis of neutron diffraction, but rather suggest a proton configuration close to the lowest energy structure predicted by Martinez et al. [J.-R. Martinez, C. E. Moen, S. Stoelen, N. L. Allan, J. of Solid State Chem. 180, 3388, (2007)]. An intense Raman active vibration at 150 cm$^{-1}$ is identified as a unique fingerprint of this proton configuration.

cond-mat.mtrl-sci↗