Free-electron Laser Radiation Research Articles

Appraising protein conformational changes by resampling time-resolved serial x-ray crystallography data.

With the development of serial crystallography at both x-ray free electron laser and synchrotron radiation sources, time-resolved x-ray crystallography is increasingly being applied to study conformational changes in macromolecules. A successful time-resolved serial crystallography study requires the growth of microcrystals, a mechanism for synchronized and homogeneous excitation of the reaction of interest within microcrystals, and tools for structural interpretation. Here, we utilize time-resolved serial femtosecond crystallography data collected from microcrystals of bacteriorhodopsin to compare results from partial occupancy structural refinement and refinement against extrapolated data. We illustrate the domain wherein the amplitude of refined conformational changes is inversely proportional to the activated state occupancy. We illustrate how resampling strategies allow coordinate uncertainty to be estimated and demonstrate that these two approaches to structural refinement agree within coordinate errors. We illustrate how singular value decomposition of a set of difference Fourier electron density maps calculated from resampled data can minimize phase bias in these maps, and we quantify residual densities for transient water molecules by analyzing difference Fourier and Polder omit maps from resampled data. We suggest that these tools may assist others in judging the confidence with which observed electron density differences may be interpreted as functionally important conformational changes.

Infrared free electron laser-irradiated polyleucine does not exert aggregates-induced aversive effects on mouse brain

Polyglutamine (polyQ) diseases are devastating neurological disorders that cannot be effectively treated. Repeat-associated non-AUG (RAN) translation has been documented in transcripts in polyQ diseases. RAN products include proteins with polyleucine (polyL) tracts. Similar to polyQ, polyL tends to aggregate, which is toxic to cells and mice. Irradiation with a free electron laser (FEL) tuned at mid-infrared wavelengths can dissociate polyQ aggregates in cultured cells. However, whether FEL dissociates the polyL is unclear. It is also unclear whether brain dysfunction caused by polyL aggregates in mice can be ameliorated by FEL irradiated polyL. Here, we show that FEL at approximately 6 μm can destroy polyL aggregates, as evidenced by scanning electron microscopy, atomic force microscopy, and dot blot analyses. Although polyL aggregates induced low viability and aberrant morphology of cultured astrocytes, FEL irradiated polyL exhibited mild defects. Likewise, the toxicity of polyL-containing microglia in vitro was ameliorated by FEL irradiation. In vivo, mice administered polyL aggregates in the cerebellum induced loss of Purkinje cells, which was ameliorated when FEL irradiated polyL was injected. These results justify the clearing of aggregates by approaches using molecular chaperones, laser irradiation, and ultrasound as a general therapeutic strategy to correct brain dysfunction by the RAN products.

Ultra-high harmonic conversion of a seeded free-electron laser via harmonic optical klystron

External seeded free-electron lasers (FELs) are compelling tools for generating fully coherent EUV and soft x-ray radiations. Echo-enabled harmonic generation (EEHG), the most typical representative of external seeded FELs, has witnessed a remarkable growth of fully coherent FELs in the last decade, continuously evolving towards higher harmonic conversions and shorter wavelengths. Ultra-high harmonic generation is imperative in the field of FELs. This paper presents a novel method for generating FEL radiation with ultra-high harmonic conversion, utilizing harmonic optical klystron in combination with EEHG. This method can effectively increase the harmonic conversion order to about 90. Theoretical analysis and numerical simulations show that intense and almost fully coherent FEL pulses can be generated with a wavelength of 3 nm. At the same time, the seed laser intensity required by this scheme is lower compared to nominal EEHG, thus facilitating the generation of high-repetition-rate seeded FELs.

Probing the Dynamic Landscape: From Static to Time-Resolved X-Ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders.

Copper (Cu), with its ability to exist in various oxidation states, notably Cu(I) and Cu(II), plays a crucial role in diverse biological redox reactions. This includes its involvement in pathways associated with oxidative stress in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Transmissible Spongiform Encephalopathies. This paper offers an overview of X-ray Absorption Spectroscopy (XAS) studies designed to elucidate the interactions between Cu ions and proteins or peptides associated with these neurodegenerative diseases. The emphasis lies on XAS specificity, revealing the local coordination environment, and on its sensitivity to Cu oxidation states. Furthermore, the paper focuses on XAS applications targeting the characterization of intermediate reaction states and explores the opportunities arising from recent advancements in time-resolved XAS at ultrabright synchrotron and Free Electron Laser radiation sources.

Three-dimensional, time-dependent simulation of tapered EUV FELs with phase shifters

In this article, we have developed and evaluated a method for obtaining extreme ultraviolet (EUV) radiation by amplifying the third harmonic of the free-electron laser (FEL) radiation using phase shifters and tapering. Simulations of self-amplified spontaneous emission (SASE) FELs and seeding schemes are presented. We have demonstrated that the combination of phase shifts and tapering results in a more efficient technique that reduces electron beam energy by half. The stability of the scheme in relation to phase shift errors has been analyzed, and the implementation of the method has been discussed. The proposed FEL design enables a decrease in facility energy and a reduction in the cost of both new and existing projects in the EUV band.

Novel correction procedure for compensating thermal contraction errors in the measurement of the magnetic field of superconducting undulator coils in a liquid helium cryostat.

Superconducting undulators (SCUs) can offer a much higher on-axis undulator field than state-of-the-art cryogenic permanent-magnet undulators with the same period and vacuum gap. The development of shorter-period and high-field SCUs would allow the free-electron laser and synchrotron radiation source community to reduce both the length of undulators and the dimensions of the accelerator. Magnetic measurements are essential for characterizing the magnetic field quality of undulators for operation in a modern light source. Hall probe scanning is so far the most mature technique for local field characterization of undulators. This article focuses on the systematic error caused by thermal contraction that influences Hall probe measurements carried out in a liquid helium cryostat. A novel procedure, based on the redundant measurement of the magnetic field using multiple Hall probes at known relative distance, is introduced for the correction of such systematic error.

High-resolution multi-mode electron and ion imaging spectrometer at SXFEL

A new multi-mode electron and ion (MEI) imaging spectrometer with two arms of VMI and COLTRIMS/VMI (velocity map imaging/cold-target recoil-ion momentum spectroscopy) is designed to combine various photoelectron and ion detection modes for experiments at Shanghai soft x-ray free-electron laser (SXFEL) facility. The experiments can be optionally operated either with both ion and electron detection in a coincidence/covariance manner (VMI arm and COLTRIMS/VMI arm), or only photoelectron/photoion is detected with the high-resolution VMI arm. The simulated resolutions for 30–150 eV photoelectrons and 3.3 eV–18.0 eV N+ and N2+ photoions are up to 1.0% and 3.1%–1.0% according to our simulation, respectively. MEI spectrometer is expected to improve the experimental abilities significantly considering the low-repetition rate of the SXFEL and to enable the investigation of a diverse range of atomic and molecular phenomena triggered by soft x-ray free electron laser irradiation.

Photon Diagnostics for the High-Gain THz FEL at PITZ

Research and development of an accelerator-based THz source prototype for pump-probe experiments at the European XFEL are ongoing at the Photo Injector Test Facility at DESY in Zeuthen (PITZ). Proof-of-principle experiments have been performed to generate a high-gain THz Free-electron Laser (FEL) based on the Self-Amplified Spontaneous Emission scheme. The FEL radiation pulses with a central wavelength of about 100 μm (3 THz) and single pulse energy of several tens μm can be generated. In this paper, we present and discuss the photon diagnostic setup for the THz FEL together with examples of diagnostic results, including pulse energy and an FEL gain curve. The upgraded photon diagnostic setup, capable of measuring pulse energy, transverse distribution, and spectral distribution, is expected to be operational in the spring of 2023.

Solving the spectral gap problem with a four-mirror bow-tie cavity in waveguide free-electron laser oscillators

The generation of intense coherent radiation pulses in the far-infrared and terahertz regimes is of considerable interest to the free-electron laser (FEL) radiation user community. At long wavelengths, the diffraction effect can be quite severe, therefore, an optical waveguide is required to confine the radiation field. However, it will also bring about some new phenomena, and the most noteworthy one is the spectral gap phenomenon: at some particular wavelengths, regardless of electron beam adjustments, the coupling efficiency and output power of waveguide FEL oscillators drop significantly. Such spectral gap has an adverse effect on experimental results since numerous experiments require continuous spectral scanning. In this paper, we propose to utilize a bow-tie cavity instead of conventional cavities to the waveguide FEL to solve the spectral gap problem. The simulation was carried out based on the parameters of FELiChEM, a newly built user facility in China. Numerical simulation code OPC combining with modified GENESIS is used to enable the modelling, for the first time, of a bow-tie cavity based FEL in the far-infrared wavelength regime. The simulation results indicate that this novel structure can effectively eliminate the spectral gaps and substantially enhance long-wavelength laser performance.

Suppressing of even harmonics in free electron lasers by modifying the energy spread of the beam

Using an analytical description of the evolution of the power of harmonics in free electron laser (FEL) undulators, we study the effect of electron beam parameters on the main characteristics of FEL radiation: the gain length, spectrum, and harmonic power. The possibility of suppressing even harmonics of the FEL as a light source in the study of materials and surfaces by analyzing the second harmonic nonlinear response (SHG) is being studied. The main factors influencing the radiation of even FEL harmonics are revealed; the influence of the beam cross section and the spread of electron energies on their radiation is analyzed. An example of a LEUTL FEL with visible light emission, which is used in studies of the optical properties of materials and the chemical state of molecules on surfaces and interfaces between media, is considered. In this context, the possibility of suppressing the second FEL harmonic is analyzed.

The Influence of Increased Electron Energy Spread on the Radiation of the Second Harmonic in Free Electron Lasers

Free electron lasers (FELs) are becoming more and more popular as sources of radiation for research purposes in many fields of science. They are frequently employed in second harmonic generation (SHG) studies. SHG is an important effect of nonlinear responses of matter to irradiation. It should be separated from the second harmonic of the radiation source, FELs, for correct analysis of the response. Using an analytical model for harmonic powers evolution in a single-pass FEL, we demonstrate the dependence of FEL harmonics on the key parameters of beams and undulators and show that it is possible to reduce the second FEL harmonic content if the energy spread of an electron beam is increased. For LEUTL FEL radiation in the visible range, we analytically demonstrate a reduction in the second harmonic power by an order of magnitude if electron energy spread is increased twice, which still allows efficient bunching at the fundamental wavelength. The method is valid regardless of the photon energy and, therefore, the absorption edge of the target material, and as such, it is valid also in the X-ray band.

Cascaded hard X-ray self-seeded free-electron laser at megahertz repetition rate

AbstractHigh-resolution X-ray spectroscopy in the sub-nanosecond to femtosecond time range requires ultrashort X-ray pulses and a spectral X-ray flux considerably larger than that presently available. X-ray free-electron laser (XFEL) radiation from hard X-ray self-seeding (HXRSS) setups has been demonstrated in the past and offers the necessary peak flux properties. So far, these systems could not provide high repetition rates enabling a high average flux. We report the results for a cascaded HXRSS system installed at the European XFEL, currently the only operating high-repetition-rate hard X-ray XFEL facility worldwide. A high repetition rate, combined with HXRSS, allows the generation of millijoule-level pulses in the photon energy range of 6–14 keV with a bandwidth of around 1 eV (corresponding to about 1 mJ eV–1 peak spectral density) at the rate of ten trains per second, each train including hundreds of pulses arriving at a megahertz repetition rate. At 2.25 MHz repetition rate and photon energies in the 6–7 keV range, we observed and characterized the heat-load effects on the HXRSS crystals, substantially altering the spectra of subsequent X-ray pulses. We demonstrated that our cascaded self-seeding scheme reduces this detrimental effect to below the detection level. This opens up exciting new possibilities in a wide range of scientific fields employing ultrafast X-ray spectroscopy, scattering and imaging techniques.

A phenomenological model of the X-ray pulse statistics of a high-repetition-rate X-ray free-electron laser.

Many coherent imaging applications that utilize ultrafast X-ray free-electron laser (XFEL) radiation pulses are highly sensitive to fluctuations in the shot-to-shot statistical properties of the source. Understanding and modelling these fluctuations are key to successful experiment planning and necessary to maximize the potential of XFEL facilities. Current models of XFEL radiation and their shot-to-shot statistics are based on theoretical descriptions of the source and are limited in their ability to capture the shot-to-shot intensity fluctuations observed experimentally. The lack of accurate temporal statistics in simulations that utilize these models is a significant barrier to optimizing and interpreting data from XFEL coherent diffraction experiments. Presented here is a phenomenological model of XFEL radiation that is capable of capturing the shot-to-shot statistics observed experimentally using a simple time-dependent approximation of the pulse wavefront. The model is applied to reproduce non-stationary shot-to-shot intensity fluctuations observed at the European XFEL, whilst accurately representing the single-shot properties predicted by FEL theory. Compared with previous models, this approach provides a simple, robust and computationally inexpensive method of generating statistical representations of XFEL radiation.

Formation of Periodic Surface Structures on Semiconductors under Mid-Infrared Free-Electron Laser Irradiation

Formation of Periodic Surface Structures on Semiconductors under Mid-Infrared Free-Electron Laser Irradiation

Dissociation process of polyalanine aggregates by free electron laser irradiation.

Polyalanine (polyA) disease-causative proteins with an expansion of alanine repeats can be aggregated. Although curative treatments for polyA diseases have not been explored, the dissociation of polyA aggregates likely reduces the cytotoxicity of polyA. Mid-infrared free electron laser (FEL) successfully dissociated multiple aggregates. However, whether the FEL dissociates polyA aggregates like other aggregates has not been tested. Here, we show that FEL at 6.1 μm experimentally weakened the extent of aggregation of a peptide with 13 alanine repeats (13A), and the irradiated 13A exerted lesser cytotoxicity to neuron-like cells than non-irradiated 13A. Then, we applied molecular dynamics (MD) simulation to follow the dissociation process by FEL. We successfully observed how the intermolecular β-sheet of polyA aggregates was dissociated and separated into monomers with helix structures upon FEL irradiation. After the dissociation by FEL, water molecules inhibited the reformation of polyA aggregates. We recently verified the same dissociation process using FEL-treated amyloid-β aggregates. Thus, a common mechanism underlies the dissociation of different protein aggregates that cause different diseases, polyA disease and Alzheimer's disease. However, MD simulation indicated that polyA aggregates are less easily dissociated than amyloid-β aggregates and require longer laser irradiation due to hydrophobic alanine repeats.

On the physics of generation of even and odd harmonics in the undulators of free electron lasers

We theoretically explore the physics of even and odd harmonics generation and radiation in undulators of single pass free electron lasers (FELs). Planar undulators are studied as a most common design. The results are obtained analytically and some of them also numerically. In the analytical form the contributions of various factors to the harmonic generation are distinguished and their effect is analyzed. The results are verified with numerical simulations and compared with reported experimental data; the data for best documented FELs in terms of harmonic generation, LEUTL and LCLS, is analyzed. The reasons for even harmonic generation are identified; we show that they differ for the spontaneous undulator radiation and for the stimulated FEL radiation. Comparative analysis is performed with various theoretical models for the FEL harmonic powers. The advantages and possibilities of amplification and radiation the second FEL harmonic in the LCLS-II FEL with variable deflection parameter is demonstrated for the harmonic lasing self-seed (HLSS) FEL design. The possibility to suppress the radiated second harmonic in a FEL by a guiding field of a weak second harmonic of the main undulator field with negative phase is shown. This can be used to reduce the reflected signal of the second harmonic generation (SHG) when the nonlinear harmonic response of the mater is investigated.

Simulations of collisional effects in an inner-shell solid-density Mg X-ray laser.

Inner-shell [Formula: see text] X-ray lasers have been created by pumping gaseous, solid, and liquid targets with the intense X-ray output of free-electron lasers (FELs). For gaseous targets lasing relies on the creation of [Formula: see text]-shell core holes on a time-scale short compared with filling via Auger decay. In the case of solid and liquid density systems, collisional effects will also be important, affecting not only populations but also line-widths, both of which impact the degree of overall gain, and its duration. However, to date, such collisional effects have not been extensively studied. We present here initial simulations using the CCFLY code of inner-shell lasing in solid-density Mg, where we self-consistently treat the effects of the incoming FEL radiation and the atomic kinetics of the Mg system, including radiative, Auger and collisional effects. We find that the combination of collisional population of the lower states of the lasing transitions and broadening of the lines precludes lasing on all but the [Formula: see text] of the initially cold system. Even assuming instantaneous turning on of the FEL pump, we find the duration of the gain in the solid system to be sub-femtosecond. This article is part of the theme issue 'Dynamic and transient processes in warm dense matter'.

Quantum description of free electron laser radiation and nonlinear amplitude equations

A relativistic quantum mechanical model to describe the quantum free electron laser dynamics has been developed. Neglecting the spin of electrons in the impacting beam, this model is based on the Klein–Gordon equation coupled to the Poisson equation for the space-charge potential and the wave equation for the transverse components of the radiation field. Furthermore, a system of coupled nonlinear envelope equations for the slowly varying amplitudes of the electron beam distribution and the radiation field has been derived. The fundamental system of basic equations has been cast into a suitable hydrodynamic formulation. In the framework of the hydrodynamic representation, a new dispersion relation has been derived and analyzed in both the quantum and the quasi-classical regimes, where the space-charge oscillations of the electron beam are taken into account.

Development of an APPLE III undulator prototype with three-dimensional force compensation for SHINE

The Shanghai high-repetition-rate XFEL and extreme light facility (SHINE) plans to install several elliptically polarizing undulators (EPUs) as afterburners behind the planar undulator section to obtain nearly saturated circularly polarized free-electron laser (FEL) radiation. Therefore, the SHINE R&D project needs to develop a 4-m-long EPU with an effective magnetic field of 1.5 T, a period of 68 mm, and a minimum gap of 3 mm. A magnetic force compensation EPU prototype has recently been built and tested at the Shanghai Synchrotron Radiation Facility (SSRF) based on the addition of permanent magnets. This prototype can realize magnetic compensation under various polarization modes in all working gaps, thereby reducing the deformation of the girders and maintaining sufficient rigidity of the mechanical structure. A girder deformation monitoring system was established to obtain real force compensation feedback. The final magnetic field measurement results meet the physical requirements, and the proposed scheme can be used as an alternative to the EPU with a high magnetic field and large magnetic force.

Ultrafast Roaming Mechanisms in Ethanol Probed by Intense Extreme Ultraviolet Free-Electron Laser Radiation: Electron Transfer versus Proton Transfer

Ultrafast H2+ and H3+ formation from ethanol is studied using pump-probe spectroscopy with an extreme ultraviolet (XUV) free-electron laser. The first pulse creates a dication, triggering H2 roaming that leads to H2+ and H3+ formation, which is disruptively probed by a second pulse. At photon energies of 28 and 32 eV, the ratio of H2+ to H3+ increases with time delay, while it is flat at a photon energy of 70 eV. The delay-dependent effect is ascribed to a competition between electron and proton transfer. High-level quantum chemistry calculations show a flat potential energy surface for H2 formation, indicating that the intermediate state may have a long lifetime. The ab initio molecular dynamics simulation confirms that, in addition to the direct emission, a small portion of H2 undergoes a roaming mechanism that leads to two competing pathways: electron transfer from H2 to C2H4O2+ and proton transfer from C2H4O2+ to H2.