The free electron laser: A single-particle classical model

1978 ◽  
Vol 21 (11) ◽  
pp. 399-404 ◽  
Author(s):  
A. Bambini ◽  
A. Renieei
Keyword(s):  
Single Particle ◽  
Free Electron ◽  
Free Electron Laser ◽  
Classical Model

scholarly journals Comparison of EMC and CM methods for orienting diffraction images in single-particle imaging experiments

IUCrJ ◽  
2021 ◽  
Vol 8 (6) ◽  
Author(s):  
Miklós Tegze ◽  
Gábor Bortel
Keyword(s):  
Intensity Distribution ◽  
Single Particle ◽  
Free Electron ◽  
Free Electron Laser ◽  
Biological Molecules ◽  
Crucial Step ◽  
X Ray ◽  
Diffraction Patterns ◽  
Particle Imaging ◽  
Single Particle Imaging

In single-particle imaging (SPI) experiments, diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. The crucial step of the data processing of SPI is finding the orientations of the recorded diffraction patterns in reciprocal space and reconstructing the 3D intensity distribution. Here, two orientation methods are compared: the expansion maximization compression (EMC) algorithm and the correlation maximization (CM) algorithm. To investigate the efficiency, reliability and accuracy of the methods at various XFEL pulse fluences, simulated diffraction patterns of biological molecules are used.

scholarly journals Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

IUCrJ ◽  
2017 ◽  
Vol 4 (5) ◽  
pp. 560-568 ◽  
Author(s):  
Carsten Fortmann-Grote ◽  
Alexey Buzmakov ◽  
Zoltan Jurek ◽  
Ne-Te Duane Loh ◽  
Liubov Samoylova ◽  
...  
Keyword(s):  
Pulse Duration ◽  
Diffraction Data ◽  
Single Particle ◽  
Free Electron ◽  
Free Electron Laser ◽  
Structural Information ◽  
X Ray ◽  
Particle Imaging ◽  
Single Particle Imaging ◽  
The Impact

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.

scholarly journals Abstract P-1: Analysis of Tick-borne Encephalitis Virus Single-particle Imaging on X-ray Free-electron Laser

2021 ◽  
Vol 11 (Suppl_1) ◽  
pp. S11-S11
Author(s):  
Grigoriy Armeev ◽  
Alexey Shaytan ◽  
Mikhail Vorovich ◽  
Alexey Egorov ◽  
Aydar Ishmukhametov ◽  
...  
Keyword(s):  
Electron Density ◽  
Single Particle ◽  
Free Electron ◽  
Free Electron Laser ◽  
Encephalitis Virus ◽  
X Ray ◽  
Tick Borne Encephalitis ◽  
Tick Borne Encephalitis Virus ◽  
Particle Imaging ◽  
Single Particle Imaging

Background: Tick-borne encephalitis virus (TBEV) is a dangerous human pathogen which envelope structure is already known from cryoEM study. TBEV mature viral particle size (~50 nm in diameter) makes it suitable for single-particle imaging (SPI) on X-ray free-electron laser (XFEL). XFEL SPI studies are at the early stages of development; thus, a well-described and conformationally homogeneous sample is required to develop approaches for experimental setup and data analysis. Here we present the image analysis results of data collected in October 2019 during the European XFEL experiment #2316. Methods: The detector was placed at 1.62 m from the injector; photon energy was around 6 keV, pulse energy 4 mJ, beam diameter ~ 500 nm. All runs were processed to detect hits with threshold filter (5th percentile of lit pixels) and further filtered to omit low-intensity images and images that lack detector modules. Filtered hits were background and geometry corrected with SPImage library and custom python scripts. Then hits were azimuthally integrated using PyFAI library. Scattering profiles were further clustered using the affinity propagation algorithm with cosine similarity metric in log space. Extracted classes were used to build averaged images. All hit profiles were fitted with model scattering to estimate the diameter of the particle. Simulated diffraction patterns were prepared using Condor from the cryoEM electron density map (EMDB ID 3752). Results: During the analysis after the filtering, only 276 clean and bright hits were collected per 135 min of injection (from 27287 hits detected via lit pixels threshold). Thus the hit rate was around ~ 2 hits/min, which is expected to rise in the future. The majority of hits correspond to the 40-50 nm particles (Fig. 1a), which is expected for TBEV. However, the exact size may vary due to solvent evaporation, ion condensation, and possible variability in the sample. Conclusion: The averaged images and their scattering profiles correlate with the simulated scattering patterns, though not ideally (Fig. 1 bc). Such discrepancy is expected due to the absence of electron density in the center of modeled viral structures.

scholarly journals Basic Reinforcement Learning Techniques to Control the Intensity of a Seeded Free-Electron Laser

Electronics ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 781 ◽  
Author(s):  
Niky Bruchon ◽  
Gianfranco Fenu ◽  
Giulio Gaio ◽  
Marco Lonza ◽  
Finn Henry O’Shea ◽  
...  
Keyword(s):  
Reinforcement Learning ◽  
Free Electron ◽  
Performance Optimization ◽  
Free Electron Laser ◽  
Classical Model ◽  
Particle Accelerator ◽  
Particle Accelerators ◽  
Seed Laser ◽  
Model Free ◽  
Performance Recovery

Optimal tuning of particle accelerators is a challenging task. Many different approaches have been proposed in the past to solve two main problems—attainment of an optimal working point and performance recovery after machine drifts. The most classical model-free techniques (e.g., Gradient Ascent or Extremum Seeking algorithms) have some intrinsic limitations. To overcome those limitations, Machine Learning tools, in particular Reinforcement Learning (RL), are attracting more and more attention in the particle accelerator community. We investigate the feasibility of RL model-free approaches to align the seed laser, as well as other service lasers, at FERMI, the free-electron laser facility at Elettra Sincrotrone Trieste. We apply two different techniques—the first, based on the episodic Q-learning with linear function approximation, for performance optimization; the second, based on the continuous Natural Policy Gradient REINFORCE algorithm, for performance recovery. Despite the simplicity of these approaches, we report satisfactory preliminary results, that represent the first step toward a new fully automatic procedure for the alignment of the seed laser to the electron beam. Such an alignment is, at present, performed manually.

Single-particle dynamics of a free-electron laser with axial field

1987 ◽  
Vol 35 (12) ◽  
pp. 5131-5136 ◽  
Author(s):  
T. P. Pandya ◽  
L. M. Bali ◽  
Usha Bakshi ◽  
Pallavi Jha
Keyword(s):  
Single Particle ◽  
Free Electron ◽  
Free Electron Laser ◽  
Particle Dynamics ◽  
Axial Field
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