arXiv subjects

Safi Rafie-Zinedine

Publications and source records attributed to Safi Rafie-Zinedine.

8 recordsLinked to original sources

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↗

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

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

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↗

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

Optical coherence properties of Kramers' rare-earth ions at the nanoscale for quantum applications

Rare-earth (RE) ion doped nano-materials are promising candidates for a range of quantum technology applications. Among RE ions, the so-called Kramers' ions possess spin transitions in the GHz range at low magnetic fields, which allows for high-bandwidth multimode quantum storage, fast qubit operations as well as interfacing with superconducting circuits. They also present relevant optical transitions in the infrared. In particular, Er$^{3+}$ has an optical transition in the telecom band, while Nd$^{3+}$ presents a high-emission-rate transition close to 890 nm. In this paper, we measure spectroscopic properties that are of relevance to using these materials in quantum technology applications. We find the inhomogeneous linewidth to be 10.7 GHz for Er$^{3+}$ and 8.2 GHz for Nd$^{3+}$, and the excited state lifetime T$_1$ to be 13.68 ms for Er$^{3+}$ and 540 $μ$s for Nd$^{3+}$. We study the dependence of homogeneous linewidth on temperature for both samples, with the narrowest linewidth being 379 kHz (T$_2$ = 839 ns) for Er$^{3+}$ measured at 3 K, and 62 kHz (T$_2$ = 5.14 $μ$s) for Nd$^{3+}$ measured at 1.6 K. Further, we investigate time-dependent homogeneous linewidth broadening due to spectral diffusion and the dependence of homogeneous linewidth on magnetic field, in order to get additional clarity of mechanisms that can influence the coherence time. In light of our results, we discuss two applications: single qubit-state readout and a Fourier-limited single photon source.

quant-ph↗

arXiv2018

Simplifying Quantum Gravity Calculations

The Einstein-Hilbert Lagrangian for gravity is non-renormalizable at loop level. However, it can be treated in the effective field theory framework which means that gravity as an effective theory can be renormalized when a proper expansion of the effective Lagrangian is made. At the same time, the Feynman rules for gravity are very complicated, although the resulting amplitudes do not have the same complications. Therefore, in this thesis we want to simplify the Feynman rules as much as possible by using the most general parameterized gauge condition, adding all possible parameterized total derivative terms and redefining the gravitational, ghosts and scalar fields in a general parameterization way. By choosing the parameters in a specific way, we obtain simplified Feynman rules, especially the triple and quadruple graviton vertices are simplified. In addition, we verify our simplified rules by calculating the amplitudes of scalar-graviton and graviton-graviton scattering at tree level using the simplified and standard Feynman rules. Finally, we show the utility of these simplified rules by calculating some one-loop diagrams for scalar-graviton scattering and comparing to the standard Feynman rules.

hep-th↗