arXiv subjects

Adrian P. Mancuso

Publications and source records attributed to Adrian P. Mancuso.

12 recordsLinked to original sources

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

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

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

The importance of temperature-dependent collision frequency in PIC simulation on nanometric density evolution of highly-collisional strongly-coupled dense plasmas

Particle-in-Cell (PIC) method is a powerful plasma simulation tool for investigating high-intensity femtosecond laser-matter interaction. However, its simulation capability at high-density plasmas around the Fermi temperature is considered to be inadequate due, among others, to the necessity of implementing atomic-scale collisions. Here, we performed a one-dimensional with three-velocity space (1D3V) PIC simulation that features the realistic collision frequency around the Fermi temperature and atomic-scale cell size. The results are compared with state-of-the-art experimental results as well as with hydrodynamic simulation. We found that the PIC simulation is capable of simulating the nanoscale dynamics of solid-density plasmas around the Fermi temperature up to $\sim$2~ps driven by a laser pulse at the moderate intensity of $10^{14-15}$~$\mathrm{W/cm^{2}}$, by comparing with the state-of-the-art experimental results. The reliability of the simulation can be further improved in the future by implementing multi-dimensional kinetics and radiation transport.

physics.plasm-ph↗

arXiv2024

Distinct transient structural rearrangement of ionized water revealed by XFEL X-ray pump X-ray probe experiment

Using X-ray free electron laser (XFEL) radiation to conduct an X-ray pump X-ray probe experiment, we studied strongly ionized water as part of our ongoing work on radiation damage. After irradiance with a pump pulse with a nominal fluence of ~$5 \times 10^5$ J/cm$^2$, we observed for pump-probe delays of 75 fs and longer an unexpected structural rearrangement, exhibiting a characteristic length scale of ~9 Å. Simulations suggest that the experiment probes a superposition of ionized water in two distinct regimes. In the first, fluences expected at the X-ray focus create nearly completely ionized water, which as a result becomes effectively transparent to the probe. In the second regime, out of focus pump radiation produces O$^{1+}$ and O$^{2+}$ ions, which rearrange due to Coulombic repulsion over 10s of fs. Importantly, structural changes in the low fluence regime have implications for the design of two-pulse X-ray experiments that aim to study unperturbed liquid samples. Our simulations account for two key observations in the experimental data: the decrease in ambient water signal and an increase in low-angle X-ray scattering. They cannot, however, account for the experimentally observed 9 Å feature. A satisfactory account of this feature presents a new challenge for theory.

physics.plasm-ph↗

arXiv2024

MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics

We describe a method to compute photon-matter interaction and atomic dynamics with X-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically computed based on changes to their electronic occupations and the free electron cloud created due to the irradiation of photons in the X-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, which reduces the number of non-bonded interactions required to compute. In combination with parallelisation through domain decomposition, large-scale molecular dynamics and ionisation induced by X-ray lasers can be followed. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters and crystals) that when exposed to an X-ray laser pulse turn into a plasma in the first few femtoseconds of the interaction. We show several examples of the applicability of the method and we quantify the sizes that the method is suitable for. For large systems, we investigate non-thermal heating and scattering of bulk water, which we compare to previous experiments. We simulate molecular dynamics of a protein crystal induced by an X-ray pump, X-ray probe scheme, and find good agreement of the damage dynamics with experiments. For single particle imaging, we simulate ultrafast dynamics of a methane cluster exposed to a femtosecond X-ray laser. In the context of coherent diffractive imaging we study the fragmentation as given by an X-ray pump X-ray probe setup to understand the evolution of radiation damage.

physics.chem-ph↗

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

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↗

arXiv2021

Nanoscale subsurface dynamics of solids upon high-intensity laser irradiation observed by femtosecond grazing-incidence x-ray scattering

Observing ultrafast laser-induced structural changes in nanoscale systems is essential for understanding the dynamics of intense light-matter interactions. For laser intensities on the order of $10^{14} \, \rm W/cm^2$, highly-collisional plasmas are generated at and below the surface. Subsequent transport processes such as heat conduction, electron-ion thermalization, surface ablation and resolidification occur at picosecond and nanosecond time scales. Imaging methods, e.g. using x-ray free-electron lasers (XFEL), were hitherto unable to measure the depth-resolved subsurface dynamics of laser-solid interactions with appropriate temporal and spatial resolution. Here we demonstrate picosecond grazing-incidence small-angle x-ray scattering (GISAXS) from laser-produced plasmas using XFEL pulses. Using multi-layer (ML) samples, both the surface ablation and subsurface density dynamics are measured with nanometer depth resolution. Our experimental data challenges the state-of-the-art modeling of matter under extreme conditions and opens new perspectives for laser material processing and high-energy-density science.

physics.plasm-ph↗

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

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 X-ray microscopy at X-ray Free-Electron Laser and Synchrotron sources

We demonstrate X-ray phase contrast microscopy performed at the European X-ray Free-Electron Laser sampled at 1.128 MHz rate. We have applied this method to image stochastic processes induced by an optical laser incident on water-filled capillaries with micrometer scale spatial resolution. The generated high speed water jet, cavitation formation and annihilation in water and glass, as well as glass explosions are observed. The comparison between XFEL and previous synchrotron MHz microscopy shows the superior contrast and spatial resolution at the XFEL over the synchrotron. This work opens up new possibilities for the characterization of dynamic stochastic systems on nanosecond to microsecond time scales at megahertz rate with object velocities up to few kilometers per second using X-ray Free-Electron Laser sources.

physics.ins-det↗