arXiv subjects

Filipe R. N. C. Maia

Publications and source records attributed to Filipe R. N. C. Maia.

18 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

Three-dimensional imaging of isolated membrane-protein complexes in vacuo with an X-ray laser

The prospect of imaging single biomolecules, viruses and cells with intense, ultrashort X-ray pulses has driven the development of X-ray free-electron lasers (XFELs). However, the weak scattering from small particles is easily swamped by background from residual gas, which has so far limited applications to strongly scattering targets such as viruses, cell organelles and cells. Here we report a three-dimensional (3D) reconstruction of an isolated 1-MDa membrane-protein complex, photosystem I (PS I), from single-particle diffraction data. PS I trimers were aerosolised by charge-reduction electrospray ionisation and injected into the European XFEL beam, with partial helium gas exchange reducing background scattering by 80%. From 32 788 diffraction patterns of single trimers in random orientations, we reconstructed the 3D electron density to a resolution of 3.8 nm, limited by the detector geometry. The disc-shaped density, about 22 nm across and 10 nm thick, matches the size of a PS I trimer in a detergent micelle and is consistent with the compaction predicted by molecular dynamics simulations of the complex in vacuo and observed in native mass spectrometry. These results show that membrane-protein complexes can be imaged in vacuo with X-ray lasers, an important step towards ultrafast diffractive imaging of single macromolecules.

physics.bio-ph↗

arXiv2025

SPRING: an effective and reliable framework for image reconstruction in single-particle Coherent Diffraction Imaging

Coherent Diffraction Imaging (CDI) is an experimental technique to gain images of isolated structures by recording the light scattered off the sample. In principle, the sample density can be recovered from the scattered light field through a straightforward Fourier Transform operation. However, only the amplitude of the field is recorded, while the phase is lost during the measurement process and has to be retrieved by means of suitable, well-established phase retrieval algorithms. In this work, we present SPRING, an analysis framework tailored to X-ray Free Electron Laser (XFEL) single-shot single-particle diffraction data that implements the Memetic Phase Retrieval method to mitigate the shortcomings of conventional algorithms. We benchmark the approach on experimental data acquired in two experimental campaigns at SwissFEL and European XFEL. Imaging results on isolated nanostructures reveal unprecedented stability and resilience of the algorithm's behavior on the input parameters, as well as the capability of identifying the solution in conditions hardly treatable so far with conventional methods. A user-friendly implementation of SPRING is released as open-source software, aiming at being a reference tool for the coherent diffraction imaging community at XFEL and synchrotron facilities.

physics.optics↗

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

Three-dimensional coherent Bragg imaging of rotating nanoparticles

Bragg Coherent Diffraction Imaging (BCDI) is a powerful strain imaging tool, often limited by beam-induced sample instability for small particles and high power densities. Here, we devise and validate an adapted diffraction volume assembly algorithm, capable of recovering three-dimensional datasets from particles undergoing uncontrolled and unknown rotations. We apply the method to gold nanoparticles which rotate under the influence of a focused coherent X-ray beam, retrieving their three-dimensional shapes and strain fields. The results show that the sample instability problem can be overcome, enabling the use of fourth generation synchrotron sources for BCDI to their full potential.

cond-mat.mtrl-sci↗

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↗

arXiv2019

Pulse-to-pulse wavefront sensing at free-electron lasers using ptychography

The pressing need for the detailed wavefront properties of ultra-bright and ultra-short pulses produced by free-electron lasers (FELs) has spurred the development of several complementary characterization approaches. Here we present a method based on ptychography that can retrieve full high-resolution complex-valued wave functions of individual pulses. Our technique is demonstrated within experimental conditions suited for diffraction experiments in their native imaging state. This lensless technique, applicable to many other short-pulse instruments, can achieve diffraction-limited resolution.

eess.IV↗

arXiv2018

Three dimensional localization of nanoscale battery reactions using soft X-ray tomography

Battery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two dimensional projections of thick material. Here, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11-nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate (LixFePO4) extracted from a battery electrode at 50% state of charge. Using a set of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nano-particles. These observations reveal multiple reaction points and intra-particle heterogeneity that highlights the importance of electrical connectivity, providing novel insight to the design of the next generation of high-performance devices.

cond-mat.mtrl-sci↗

arXiv2016

Nanosurveyor: a framework for real-time data processing

Scientists are drawn to synchrotrons and accelerator based light sources because of their brightness, coherence and flux. The rate of improvement in brightness and detector technology has outpaced Moore's law growth seen for computers, networks, and storage, and is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality. Here we present an integrated software/algorithmic framework designed to capitalize on high throughput experiments, and describe the streamlined processing pipeline of ptychography data analysis. The pipeline provides throughput, compression, and resolution as well as rapid feedback to the microscope operators.

physics.ins-det↗

arXiv2016

SHARP: a distributed, GPU-based ptychographic solver

Ever brighter light sources, fast parallel detectors, and advances in phase retrieval methods, have made ptychography a practical and popular imaging technique. Compared to previous techniques, ptychography provides superior robustness and resolution at the expense of more advanced and time consuming data analysis. By taking advantage of massively parallel architectures, high-throughput processing can expedite this analysis and provide microscopists with immediate feedback. These advances allow real-time imaging at wavelength limited resolution, coupled with a large field of view. Here, we introduce a set of algorithmic and computational methodologies used at the Advanced Light Source, and DOE light sources packaged as a CUDA based software environment named SHARP (http://camera.lbl.gov/sharp), aimed at providing state-of-the-art high-throughput ptychography reconstructions for the coming era of diffraction limited light sources.

physics.data-an↗

arXiv2006

Femtosecond Diffractive Imaging with a Soft-X-ray Free-Electron Laser

Theory predicts that with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus, or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft X-ray free-electron laser. An intense 25 fs, 4 10^13 W/cm^2 pulse, containing 10^12 photons at 32 nm wavelength, produced a coherent diffraction pattern from a nano-structured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling, shows no measurable damage, and extends to diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one.

physics.optics↗