Engineering topics

Sikorski, Marcin

Publications and source records attributed to Sikorski, Marcin.

10 records

DOE OSTI2024

Resolving Nonequilibrium Shape Variations among 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 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 nonequilibrium 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” among 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.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers

The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2022

Ultrafast structural response of shock‐compressed plagioclase

Abstract Meteor impacts can induce unique pressure‐dependent structural changes in minerals due to the propagation of shock waves. Plagioclase—ubiquitous throughout the Earth’s crust, extraterrestrial bodies, and meteorites—is commonly used for reconstructing the impact history and conditions of the parent bodies. However, there have been unresolved inconsistencies in the interpretation of shock transformations across previous studies: The pressure at which amorphization begins and the process by which it occurs is the subject of ongoing debate. Here, we utilize time‐resolved in situ X‐ray diffraction (XRD) to probe the phase transformation pathway of plagioclase during shock compression at a sub‐nanosecond timescale. Direct amorphization begins at pressures much lower than what was previously assumed, just above the Hugoniot elastic limit of 5 GPa, with full amorphization to a high‐density amorphous phase, observed at 32(10) GPa and 20 ns. Upon release, the material partially recrystallizes back into the original structure, demonstrating a memory effect.

58 GEOSCIENCES↗

DOE OSTI2022

Unsupervised learning approaches to characterizing 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 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–maximize–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.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

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

Single particle imaging at x-ray free electron lasers (XFELs) has the potential to determine the structure and dynamics of single biomolecules at room temperature. Two major hurdles have prevented this potential from being reached, namely, the collection of sufficient high-quality diffraction patterns and robust computational purification to overcome structural heterogeneity. We report the breaking of both of these barriers using gold nanoparticle test samples, recording around 10 million diffraction patterns at the European XFEL and structurally and orientationally sorting the patterns to obtain better than 3-nm-resolution 3D reconstructions for each of four samples. With these new developments, integrating advancements in x-ray sources, fast-framing detectors, efficient sample delivery, and data analysis algorithms, we illuminate the path towards sub-nanometer biomolecular imaging. The methods developed here can also be extended to characterize ensembles that are inherently diverse to obtain their full structural landscape.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Femtosecond electronic structure response to high intensity XFEL pulses probed by iron X-ray emission spectroscopy

We report the time-resolved femtosecond evolution of the K-shell X-ray emission spectra of iron during high intensity illumination of X-rays in a micron-sized focused hard X-ray free electron laser (XFEL) beam. Detailed pulse length dependent measurements revealed that rapid spectral energy shift and broadening started within the first 10 fs of the X-ray illumination at intensity levels between 10 17 and 10 18 W cm -2 . We attribute these spectral changes to the rapid evolution of high-density photoelectron mediated secondary collisional ionization processes upon the absorption of the incident XFEL radiation. These fast electronic processes, occurring at timescales well within the typical XFEL pulse durations (i.e., tens of fs), set the boundary conditions of the pulse intensity and sample parameters where the widely-accepted ‘probe-before-destroy’ measurement strategy can be adopted for electronic-structure related XFEL experiments.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2020

Femtosecond laser produced periodic plasma in a colloidal crystal probed by XFEL radiation

With the rapid development of short-pulse intense laser sources, studies of matter under extreme irradiation conditions enter further unexplored regimes. In addition, an application of X-ray Free-Electron Lasers (XFELs) delivering intense femtosecond X-ray pulses, allows to investigate sample evolution in IR pump - X-ray probe experiments with an unprecedented time resolution. Here we present a detailed study of the periodic plasma created from the colloidal crystal. Both experimental data and theory modeling show that the periodicity in the sample survives to a large extent the extreme excitation and shock wave propagation inside the colloidal crystal. This feature enables probing the excited crystal, using the powerful Bragg peak analysis, in contrast to the conventional studies of dense plasma created from bulk samples for which probing with Bragg diffraction technique is not possible. X-ray diffraction measurements of excited colloidal crystals may then lead towards a better understanding of matter phase transitions under extreme irradiation conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

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 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.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Double-pulse speckle contrast correlations with near Fourier transform limited free-electron laser light using hard X-ray split-and-delay

Abstract The ability to deliver two coherent X-ray pulses with precise time-delays ranging from a few femtoseconds to nanoseconds enables critical capabilities of probing ultra-fast phenomena in condensed matter systems at X-ray free electron laser (FEL) sources. Recent progress made in the hard X-ray split-and-delay optics developments now brings a very promising prospect for resolving atomic-scale motions that were not accessible by previous time-resolved techniques. Here, we report on characterizing the spatial and temporal coherence properties of the hard X-ray FEL beam after propagating through split-and-delay optics. Speckle contrast analysis of small-angle scattering measurements from nanoparticles reveals well-preserved transverse coherence of the beam. Measuring intensity fluctuations from successive X-ray pulses also reveals that only single or double temporal modes remain in the transmitted beam, corresponding to nearly Fourier transform limited pulses.

42 ENGINEERING↗

DOE OSTI2020

Vibrational wavepacket dynamics in Fe carbene photosensitizer determined with femtosecond X-ray emission and scattering

Abstract The non-equilibrium dynamics of electrons and nuclei govern the function of photoactive materials. Disentangling these dynamics remains a critical goal for understanding photoactive materials. Here we investigate the photoinduced dynamics of the [Fe(bmip) 2 ] 2+ photosensitizer, where bmip = 2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine, with simultaneous femtosecond-resolution Fe Kα and Kβ X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS). This measurement shows temporal oscillations in the XES and XSS difference signals with the same 278 fs period oscillation. These oscillations originate from an Fe-ligand stretching vibrational wavepacket on a triplet metal-centered ( 3 MC) excited state surface. This 3 MC state is populated with a 110 fs time constant by 40% of the excited molecules while the rest relax to a 3 MLCT excited state. The sensitivity of the Kα XES to molecular structure results from a 0.7% average Fe-ligand bond length shift between the 1 s and 2p core-ionized states surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗