arXiv subjects

Henry N. Chapman

Publications and source records attributed to Henry N. Chapman.

At least 19 recordsLinked to original sources

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↗

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

3D atomic structure determination with ultrashort-pulse MeV electron diffraction

Understanding structure at the atomic scale is fundamental for the development of materials with improved properties. Compared to other probes providing atomic resolution, electrons offer the strongest interaction in combination with minimal radiation damage. Here, we report the successful implementation of MeV electron diffraction for ab initio 3D structure determination at atomic resolution. Using ultrashort electron pulses from the REGAE accelerator, we obtained high-quality diffraction data from muscovite and $1T-TaS_2$, enabling structure refinements according to the dynamical scattering theory and the accurate determination of hydrogen atom positions. The increased penetration depth of MeV electrons allows for structure determination from samples significantly thicker than those typically applicable in electron diffraction. These findings establish MeV electron diffraction as a viable approach for investigating a broad range of materials, including nanostructures and radiation-sensitive compounds, and open up new opportunities for in-situ and time-resolved experiments.

cond-mat.mtrl-sci↗

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

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↗

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

DriftRec: Adapting diffusion models to blind JPEG restoration

In this work, we utilize the high-fidelity generation abilities of diffusion models to solve blind JPEG restoration at high compression levels. We propose an elegant modification of the forward stochastic differential equation of diffusion models to adapt them to this restoration task and name our method DriftRec. Comparing DriftRec against an $L_2$ regression baseline with the same network architecture and state-of-the-art techniques for JPEG restoration, we show that our approach can escape the tendency of other methods to generate blurry images, and recovers the distribution of clean images significantly more faithfully. For this, only a dataset of clean/corrupted image pairs and no knowledge about the corruption operation is required, enabling wider applicability to other restoration tasks. In contrast to other conditional and unconditional diffusion models, we utilize the idea that the distributions of clean and corrupted images are much closer to each other than each is to the usual Gaussian prior of the reverse process in diffusion models. Our approach therefore requires only low levels of added noise and needs comparatively few sampling steps even without further optimizations. We show that DriftRec naturally generalizes to realistic and difficult scenarios such as unaligned double JPEG compression and blind restoration of JPEGs found online, without having encountered such examples during training.

eess.IV↗

arXiv2024

Development of crystal optics for Multi-Projection X-ray Imaging for synchrotron and XFEL sources

X-ray Multi-Projection Imaging (XMPI) is an emerging technology that allows for the acquisition of millions of 3D images per second in samples opaque to visible light. This breakthrough capability enables volumetric observation of fast stochastic phenomena, which were inaccessible due to the lack of a volumetric X-ray imaging probe with kHz to MHz repetition rate. These include phenomena of industrial and societal relevance such as fractures in solids, propagation of shock waves, laser-based 3D printing, or even fast processes in the biological domain. Indeed, the speed of traditional tomography is limited by the shear forces caused by rotation, to a maximum of 1000 Hz in state-of-the-art tomography. Moreover, the shear forces can disturb the phenomena in observation, in particular with soft samples or sensitive phenomena such as fluid dynamics. XMPI is based on splitting an X-ray beam to generate multiple simultaneous views of the sample, therefore eliminating the need for rotation. The achievable performances depend on the characteristics of the X-ray source, the detection system, and the X-ray optics used to generate the multiple views. The increase in power density of the X-ray sources around the world now enables 3D imaging with sampling speeds in the kilohertz range at synchrotrons and megahertz range at X-ray Free-Electron Lasers (XFELs). Fast detection systems are already available, and 2D MHz imaging was already demonstrated at synchrotron and XFEL. In this work, we explore the properties of X-ray splitter optics and XMPI schemes that are compatible with synchrotron insertion devices and XFEL X-ray beams. We describe two possible schemes designed to permit large samples and complex sample environments. Then, we present experimental proof of the feasibility of MHz-rate XMPI at the European XFEL.

physics.ins-det↗

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

Live Iterative Ptychography with projection-based algorithms

In this work, we demonstrate that the ptychographic phase problem can be solved in a live fashion during scanning, while data is still being collected. We propose a generally applicable modification of the widespread projection-based algorithms such as Error Reduction (ER) and Difference Map (DM). This novel variant of ptychographic phase retrieval enables immediate visual feedback during experiments, reconstruction of arbitrary-sized objects with a fixed amount of computational resources, and adaptive scanning. By building upon the Real-Time Iterative Spectrogram Inversion (RTISI) family of algorithms from the audio processing literature, we show that live variants of projection-based methods such as DM can be derived naturally and may even achieve higher-quality reconstructions than their classic non-live counterparts with comparable effective computational load.

eess.IV↗

arXiv2023

Structural pathways for ultrafast melting of optically excited thin polycrystalline Palladium films

Due to its extremely short timescale, the non-equilibrium melting of metals is exceptionally difficult to probe experimentally. The knowledge of melting mechanisms is thus based mainly on the results of theoretical predictions. This work reports on the investigation of ultrafast melting of thin polycrystalline Pd films studied by optical laser pump - X-ray free-electron laser probe experiments and molecular-dynamics simulations. By acquiring X-ray diffraction snapshots with sub-picosecond resolution, we capture the sample's atomic structure during its transition from the crystalline to the liquid state. Bridging the timescales of experiments and simulations allows us to formulate a realistic microscopic picture of melting. We demonstrate that the existing models of strongly non-equilibrium melting, developed for systems with relatively weak electron-phonon coupling, remain valid even for ultrafast heating rates achieved in femtosecond laser-excited Pd. Furthermore, we highlight the role of pre-existing and transiently generated crystal defects in the transition to the liquid state.

cond-mat.mtrl-sci↗

arXiv2023

Ab Initio Spatial Phase Retrieval via Intensity Triple Correlations

Second-order intensity correlations from incoherent emitters can reveal the Fourier transform modulus of their spatial distribution, but retrieving the phase to enable completely general Fourier inversion to real space remains challenging. Phase retrieval via the third-order intensity correlations has relied on special emitter configurations which simplified an unaddressed sign problem in the computation. Without a complete treatment of this sign problem, the general case of retrieving the Fourier phase from a truly arbitrary configuration of emitters is not possible. In this paper, a general method for ab initio phase retrieval via the intensity triple correlations is described. Simulations demonstrate accurate phase retrieval for clusters of incoherent emitters which could be applied to imaging stars or fluorescent atoms and molecules. With this work, it is now finally tractable to perform Fourier inversion directly and reconstruct images of arbitrary arrays of independent emitters via far-field intensity correlations alone.

physics.optics↗

arXiv2023

Megahertz X-ray Multi-projection imaging

X-ray time-resolved tomography is one of the most popular X-ray techniques to probe dynamics in three dimensions (3D). Recent developments in time-resolved tomography opened the possibility of recording kilohertz-rate 3D movies. However, tomography requires rotating the sample with respect to the X-ray beam, which prevents characterization of faster structural dynamics. Here, we present megahertz (MHz) X-ray multi-projection imaging (MHz-XMPI), a technique capable of recording volumetric information at MHz rates and micrometer resolution without scanning the sample. We achieved this by harnessing the unique megahertz pulse structure and intensity of the European X-ray Free-electron Laser with a combination of novel detection and reconstruction approaches that do not require sample rotations. Our approach enables generating multiple X-ray probes that simultaneously record several angular projections for each pulse in the megahertz pulse burst. We provide a proof-of-concept demonstration of the MHz-XMPI technique's capability to probe 4D (3D+time) information on stochastic phenomena and non-reproducible processes three orders of magnitude faster than state-of-the-art time-resolved X-ray tomography, by generating 3D movies of binary droplet collisions. We anticipate that MHz-XMPI will enable in-situ and operando studies that were impossible before, either due to the lack of temporal resolution or because the systems were opaque (such as for MHz imaging based on optical microscopy).

eess.IV↗

arXiv2023

Online dynamic flat-field correction for MHz Microscopy data at European XFEL

The X-ray microscopy technique at the European X-ray free-electron laser (EuXFEL), operating at a MHz repetition rate, provides superior contrast and spatial-temporal resolution compared to typical microscopy techniques at other X-ray sources. In both online visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of XFEL sources hinders the use of existing flat-flied normalization methods during MHz X-ray microscopy experiments. Here, we present an online dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images. The method is used for the normalization of individual X-ray projections and has been implemented as an online analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.

physics.ins-det↗

arXiv2023

Absolute spectral metrology of XFEL pulses using diffraction in crystals

At modern X-ray sources, such as synchrotrons and X-ray Free-Electron Lasers (XFELs), it is important to measure the absolute value of the photon energy directly. Here, a method for absolute spectral metrology is presented. A photon energy estimation method based on the spectral measurements and rocking of diffracting crystals is presented. The photon energy of SASE1 channel of the European XFEL was measured, and the benefits and applications of the precise photon energy evaluation are discussed.

physics.ins-det↗

arXiv2022

Decreasing ultrafast X-ray pulse durations with saturable absorption and resonant transitions

Saturable absorption is a nonlinear effect where a material's ability to absorb light is frustrated due to a high influx of photons and the creation of electron vacancies. Experimentally induced saturable absorption in copper revealed a reduction in the temporal duration of transmitted X-ray laser pulses, but a complete understanding of this process is still missing. In this computational work, we employ non-local thermodynamic equilibrium plasma simulations to study the interaction of femtosecond X-rays and copper. Following the onset of frustrated absorption, we find that a $K\text{--}M$ resonant transition occurring at highly charged states turns copper opaque again. The changes in absorption generate a transient transparent window responsible for the shortened transmission signal. We also propose using fluorescence induced by the incident beam as an alternative source to achieve shorter X-ray pulses. Intense femtosecond X-ray pulses are valuable to probe the structure and dynamics of biological samples or to reach extreme states of matter. Shortened pulses could be relevant for emerging imaging techniques.

physics.plasm-ph↗