Pohang Accelerator Laboratory Research Articles

Beagle: a near-edge X-ray absorption fine-structure spectroscopy data processing solution for beamline experiments at Pohang Accelerator Laboratory.

Near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy is a powerful tool for identifying chemical bonding states at synchrotron radiation facilities. Advances in new materials require researchers in both academia and industry to measure tens to hundreds of samples during the available beam time on a synchrotron beamline, which is typically allocated to users. Automated measurement methods, along with analysis software, have been developed for beamlines. Automated measurements facilitate high-throughput experiments and accumulate vast amounts of measured spectral data. The analysis software supports various functions for analyzing the experimental data; however, these analysis methods are complicated, and learning them can be time-consuming. To process large amounts of spectral data, a new analysis software, dedicated to NEXAFS spectroscopy, that is easy to use and can provide results in a short time is desired. Herein, the development of Beagle is described, software calculating molecular orientation from NEXAFS spectroscopy data that can report results in a short time comparable with that required to measure one sample at the beamline. It was designed to progress in a single sequence from data loading to the printing of the results with a `click of a button'. The functions of the software include recognizing the dataset, correcting the background, normalizing the plot, calculating the electron yield and determining the molecular orientation. The analysis results can be saved as {\tt{.txt}} files (spectral data), {\tt{.pdf}} files (graphic images) and Origin files (spectral data and graphic images).

Measurement of the flux-weighted average cross section for the \(^{186}\)W\((\gamma,p)^{185}\)Ta reaction at the bremsstrahlung end-point energy of 70 MeV

Abstract. The flux-weighted average cross section for the 186W(γ,p)185Ta reaction induced with 70 MeV bremsstrahlung end-point energy was measured using the activation method in combination with off-line gamma activity measurement. The 27Al(γ,2pn)24Na monitor reaction was used for the determination of the bremsstrahlung flux. The bremsstrahlung photons used to produce the photonuclear reactions were generated from a thin tungsten (W) converter by bombardment with a 70 MeV electron beam. The experimental flux-weighted average cross section is compared with the theoretical prediction, for which the absolute cross section was calculated using the TALYS 1.95 code and the bremsstrahlung spectrum was simulated using the computer program MCNPX. The present experiment was carried out at the 100 MeV electron linac of the Pohang Accelerator Laboratory, POSTECH, Pohang, Korea.

Generation of time-synchronized two-color X-ray free-electron laser pulses using phase shifters

To optimize the intensity of X-ray free-electron lasers (XFELs), phase shifters, oriented in phase with the phases of the XFEL pulse and electron beam, are typically installed at undulator lines. Although a π-offset between the phases (i.e., an “out-of-phase” configuration) can suppress the XFEL intensity at resonant frequencies, it can also generate a side-band spectrum, which results in a two-color XFEL pulse; the dynamics of such a pulse can be described using the spontaneous radiation or low gain theory. This attributes of this two-color XFEL pulse can be amplified (log-scale amplification) through an undulator line with out-of-phase phase shifters. In this study, the features of two-color XFEL pulses were evaluated through theory, simulations and experiments performed at Pohang Accelerator Laboratory X-ray Free Electron Laser. The XFEL gain slope and energy separation between the two-color spectral peaks were consistent through theoretical expectation, and the results of simulation and experiment. The experimentally determined two-color XFEL pulse energy was 250 μJ at a photon energy of 12.38 keV with a separation of 60 eV.

Observing ice structure of micron-sized vapor-deposited ice with an x-ray free-electron laser.

The direct observation of the structure of micrometer-sized vapor-deposited ice is performed at Pohang Accelerator Laboratory x-ray free electron laser (PAL-XFEL). The formation of micrometer-sized ice crystals and their structure is important in various fields, including atmospheric science, cryobiology, and astrophysics, but understanding the structure of micrometer-sized ice crystals remains challenging due to the lack of direct observation. Using intense x-ray diffraction from PAL-XFEL, we could observe the structure of micrometer-sized vapor-deposited ice below 150 K with a thickness of 2-50 μm grown in an ultrahigh vacuum chamber. The structure of the ice grown comprises cubic and hexagonal sequences that are randomly arranged to produce a stacking-disordered ice. We observed that ice with a high cubicity of more than 80% was transformed to partially oriented hexagonal ice when the thickness of the ice deposition grew beyond 5 μm. This suggests that precise temperature control and clean deposition conditions allow μm-thick ice films with high cubicity to be grown on hydrophilic Si3N4 membranes. The low influence of impurities could enable in situ diffraction experiments of ice nucleation and growth from interfacial layers to bulk ice.

Sample Delivery Systems for Serial Femtosecond Crystallography at the PAL-XFEL

Serial femtosecond crystallography (SFX) using an X-ray free electron laser (XFEL) enables the determination of room-temperature structures without causing radiation damage. Using an optical pump-probe or mix-and-injection, SFX enables the intermediate state visualization of a molecular reaction. In SFX experiments, serial and stable microcrystal delivery to the X-ray interaction point is vital for reasonable data collection and efficient beam time. The Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL) facility established SFX instruments at a nanocrystallography and coherent imaging (NCI) experimental station. Various sample delivery methods, including injection, fixed-target scanning, and hybrid methods, have been developed and applied to collect XFEL diffraction data. Herein, we report the currently available sample delivery methods for SFX at the NCI experimental station at the PAL-XFEL. This article will help PAL-XFEL users access the SFX system for their experiments.

X-ray free electron laser studies of electron and phonon dynamics of graphene adsorbed on copper

We report optical pumping and x-ray absorption spectroscopy experiments at the Pohang Accelerator Laboratory free electron laser that probes the electron dynamics of a graphene monolayer adsorbed on copper in the femtosecond regime. By analyzing the results with ab initio theory we infer that the excitation of graphene is dominated by indirect excitation from hot electron-hole pairs created in the copper by the optical laser pulse. However, once the excitation is created in graphene, its decay follows a similar path as in many previous studies of graphene adsorbed on semiconductors, i.e., rapid excitation of strongly coupled optical phonons and eventual thermalization. It is likely that the lifetime of the hot electron-hole pairs in copper governs the lifetime of the electronic excitation of the graphene.Received 21 November 2022Accepted 26 January 2023DOI:https://doi.org/10.1103/PhysRevMaterials.7.024005©2023 American Physical SocietyPhysics Subject Headings (PhySH)Research AreasElectron emissionPhysical SystemsGrapheneTechniquesMolecular dynamicsX-ray absorption spectroscopyCondensed Matter, Materials & Applied Physics

Imaging optimisation process of human lung tissue using synchrotron radiation microcomputed tomography in PLS‐II

AbstractSynchrotron radiation microcomputed tomography (SR‐μCT) can provide non‐destructive three‐dimensional investigation for soft tissue with high resolution. The aim of this study is to evaluate technical improvements in microcomputed tomographic imaging of human lung tissue using a synchrotron radiation source at the 6C biomedical beamline. SR‐μCT images of excised human lung tissue (6 mm vertically and 10 mm horizontally sized) were explored at the 6C biomedical beamline in the Pohang accelerator laboratory (Pohang, Republic of Korea) using phase retrieval methods with a modified Bronnikov algorithm. Experimental data collection was performed with changes in the following conditions: the presence of a graphite attenuator, sample to detector distance, the presence of different scintillators and increasing pixel sizes. We identified that the resolution of lung tissue images was sufficiently enhanced when the graphite attenuator was not applied, 550 mm of sample to detector distance, with Cadmium tungsten (CdWO4) scintillator and twice binning of the pixel data and could be comparable with images from pathologic examination. Refinement of SR‐μCT techniques for soft tissue originating from the human body would advance the potential clinical application of synchrotron radiation in the near future.

Measurement of neutron capture cross sections for the 174Yb(n,γ)175Yb reaction at thermal and epithermal energies

Herein, we measured the thermal neutron capture cross section (σ0) and resonance integral (I0) of the 174Yb(n,γ)175Yb reaction relative to those of the reference reaction 197Au(n,γ)198Au. Measurements were conducted based on the activation method using pulsed neutrons combined with the Cd ratio method and offline γ-ray spectrometry. Pulsed neutrons were generated on a 100 MeV electron linac of the Pohang Accelerator Laboratory, Korea. Yb samples and Au monitors were irradiated with and without a 0.5 mm Cd cover to absorb thermal neutrons. The neutron flux was determined via the 115In(n,γ)116mIn reaction. The induced activities of the reaction products were measured using a gamma spectrometer based on a well-calibrated HPGe detector. For the 174Yb(n,γ)175Yb reaction, the thermal neutron capture cross section and resonance integral cross-section were obtained as σ0,Yb = 70.5 ± 4.2 b and I0,Yb = 54.1 ± 4.2 b, relative to the corresponding values of σ0,Au = 98.65 ± 0.09 b and I0,Au = 1550 ± 28 b for the 197Au(n,γ)198Au reference reaction. The obtained results were compared with the measured and evaluated data.

Study and improvements of a radially coupled coaxial Fast Faraday cup design toward lower intensity beams

A radially coupled coaxial fast Faraday cup design was presented in Carneiro et al. [Int. J. Mod. Phys. A 34(36), 1942013 (2019)] for high-intensity non-relativistic proton beams. In this work, we discuss a modification of that design in the context of a relatively lower intensity ion beam for longitudinal charge profile measurements. Particle-in-cell and time domain electromagnetic simulations of the new design with a focus on avoiding field dilution while generating enough signal for relatively lower intensity ion beams at the upcoming High Current Injector Program at the Inter-University Accelerator Center, New Delhi [A. Roy, Curr. Sci. 76(2), 149–153 (1999); Kanjilal et al., in 3rd Asian Particle Accelerator Conference (Pohang Accelerator Laboratory, 2004), p. 73], is discussed. Profile distortions from secondary electron emission are estimated, and strategies to suppress them are discussed.

Isomeric yield ratio of 115m,gCd in the 116Cd(γ,n) and 116Cd(n,2n) reactions

The isomeric yield ratio (IR) of 115m,gCd in the 116Cd(γ,n) reaction at the bremsstrahlung endpoint energies of 70 and 75 MeV and in the 116Cd(n,2n) reaction at the average neutron energies (<En > ) of 21.4 and 30.1 MeV were measured via an offline γ -ray spectrometric technique. The bremsstrahlung energies were produced by impinging the electron beam energies of 70 and 75 MeV on a thin W-target at the Pohang Accelerator Laboratory, Korea. The neutron beams were obtained from the 9Be(p,n) reaction with the proton energies of 35 and 45 MeV using the MC-50 cyclotron at the Korean Institute of Radiological and Medical Sciences. The IR values at different bremsstrahlung and neutron energies were also calculated from the cross-section values of the TENDL-2019 library based on the TALYS-1.9 code. The theoretical values agreed with the experimental data for the bremsstrahlung endpoint energies but were slightly higher for all neutron energies. The current and literature data showed that in both the 116Cd(γ,n) and 116Cd(n,2n) reactions, the IR value of 115m,gCd increases with the projectile energy, indicating the role of excitation energy. However, the experimental and theoretical IR values at the same excitation energy were significantly higher for the 116Cd(n,2n) reaction than that for the 116Cd(γ,n) reaction, highlighting the role of compound nucleus spin.

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

The bioactive lysophospholipid sphingosine-1-phosphate (S1P) acts via five different subtypes of S1P receptors (S1PRs) - S1P1-5. S1P5 is predominantly expressed in nervous and immune systems, regulating the egress of natural killer cells from lymph nodes and playing a role in immune and neurodegenerative disorders, as well as carcinogenesis. Several S1PR therapeutic drugs have been developed to treat these diseases; however, they lack receptor subtype selectivity, which leads to side effects. In this article, we describe a 2.2 Å resolution room temperature crystal structure of the human S1P5 receptor in complex with a selective inverse agonist determined by serial femtosecond crystallography (SFX) at the Pohang Accelerator Laboratory X-Ray Free Electron Laser (PAL-XFEL) and analyze its structure-activity relationship data. The structure demonstrates a unique ligand-binding mode, involving an allosteric sub-pocket, which clarifies the receptor subtype selectivity and provides a template for structure-based drug design. Together with previously published S1PR structures in complex with antagonists and agonists, our structure with S1P5-inverse agonist sheds light on the activation mechanism and reveals structural determinants of the inverse agonism in the S1PR family.

Performance Measurements of Photodiodes for X-Ray Detection

The X-ray free-electron laser (XFEL) at the Pohang Accelerator Laboratory (PAL), Pohang, South Korea, provides X-ray energies of up to 15 keV depending on the experimental purpose. Silicon-based devices have been used as diagnostic devices and detectors for X-rays in experimental stations. Considering recent domestic and international circumstances, developing silicon-based detectors in-house is necessary. We developed a silicon p-intrinsic-n (PIN) photodiode (PD) for X-ray detection, and its performance was investigated and compared with that of a commercial PD used in the PAL-XFEL. The PD was designed to be 1 cm <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\times1$ </tex-math></inline-formula> cm in size, and it used the junction side for signal readout and the ohmic side for X-ray entrance. Considering the absorption length of 12-keV X-rays suitable for crystallography, a 500- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$ {\mu }\text{m}$ </tex-math></inline-formula> -thick silicon wafer with a high resistivity was used for PD fabrication. It has a guard ring, an n+ edge field shaper, and an antireflection coating (ARC) and is available in four different types based on the metal structure of the junction and ohmic sides. We present here the electrical characteristics of the PDs. The depletion voltage at which the bulk of the PD is fully depleted was determined to be 119.7 ± 8.2 V from bulk capacitance measurements, and the operation voltage of the PD was set to 200 V. PDs with leakage currents less than 30 nA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at the operation voltage were chosen for performance measurements. The signal-to-noise ratio (SNR) with a Sr-90 radioactive source corresponding to the minimum ionizing particle (MIP) and the quantum efficiency (QE) for wavelengths of 300–1000 nm were measured. Beam tests were conducted at the PAL-XFEL using 600-, 900-, and 1200-eV X-rays where the responses to ultrahigh brightness and ultrashort X-ray pulses were checked. The energy resolutions were measured using gamma-ray radioactive sources, Am-241 (59.5 keV), and Ba-133 (31.0 and 81.0 keV). The differences in performance among the PD types are presented herein in terms of the electrical characteristics, SNR, QE, response to X-ray pulses, and energy resolutions. The results of the fabricated PDs were also compared with those of a commercial PD.

Multiparticle natSr(γ, ) reactions induced with bremsstrahlung end-point energies of 55, 60, and 65 MeV * *Supported by the National Research Foundation of Korea through a grant provided by the Ministry of Science and ICT (NRF-2017R1D1A1B03030484, NRF-2018R1A6A1A06024970)

This study measured the yields of the radionuclides 82Sr, 83(m+g)Sr, 85mSr, 85gSr, 87mSr, 81(g+0.976m)Rb,82mRb,83gRb,84(m+g)Rb, and 86(m+g)Rb produced in natSr(γ, xnyp) multiparticle reactions with bremsstrahlung end-point energies of 55, 60, and 65 MeV. The bremsstrahlung radiation was generated using the 100-MeV electron linear accelerator at the Pohang Accelerator Laboratory, Korea, and the reaction yields were derived from the induced activitiesmeasured using off-line γ-ray spectrometry. To obtain accurate experimental results, we performed the necessary γ-rayinterference corrections. The experimental results were compared with the theoretical predictions obtained usingthe TALYS-1.95 statistical nuclear model code. The calculations were performed using six different level-density models to ascertain which model best fitted the experimental results. The dependence of the reaction yield on the incident bremsstrahlung energy and on the number of nucleons emitted by the photonuclear reactions was also investigated.

Preliminary XFEL data from spontaneously grown endo-1,4-β-xylanase crystals from Hypocrea virens.

The enzymatic degradation of semi-cellulosic substrates has recently received immense attention. The enzyme endo-1,4-β-xylanase is essential for the complete digestion of complex and heterogeneous hemicellulose. Here, the purification, crystallization and preliminary X-ray free-electron laser (XFEL) diffraction analysis of endo-1,4-β-xylanase from the fungus Hypocrea virens (HviGH11) are reported. Codon-optimized HviGH11 was overexpressed in Escherichia coli and spontaneously crystallized after His-tag purification and concentration. Preliminary XFEL diffraction data were collected at the Pohang Accelerator Laboratory XFEL (PAL-XFEL). A total of 1021 images containing Bragg peaks were obtained and indexed. The HviGH11 crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 43.80, b = 51.90, c = 94.90 Å. Using 956 diffraction patterns, the phasing problem was solved and an initial model structure of HviGH11 was obtained.

Slow Phase Transition-Induced Scan Rate Dependence of Spin Crossover in a Two-Dimensional Supramolecular Fe(III) Complex

Slow Phase Transition-Induced Scan Rate Dependence of Spin Crossover in a Two-Dimensional Supramolecular Fe(III) Complex

Recent Progress of the PAL-XFEL

The X-ray free-electron laser of the Pohang Accelerator Laboratory (PAL-XFEL) was opened to users in 2017. Since then, significant progress has been made in PAL-XFEL operation and beamline experiments. This includes increasing the FEL pulse energy, increasing the FEL photon energy, generating self-seeding FEL, and trials of two-color operation. In the beamline, new instruments or endstations have been added or are being prepared. Overall, beamline operation has been stabilized since its initiation, which has enabled excellent scientific results through efficient user experiments. In this paper, we describe details of the recent progress of the PAL-XFEL.

Development of an experimental apparatus to observe ultrafast phenomena by tender X-ray absorption spectroscopy at PAL-XFEL.

Understanding the ultrafast dynamics of molecules is of fundamental importance. Time-resolved X-ray absorption spectroscopy (TR-XAS) is a powerful spectroscopic technique for unveiling the time-dependent structural and electronic information of molecules that has been widely applied in various fields. Herein, the design and technical achievement of a newly developed experimental apparatus for TR-XAS measurements in the tender X-ray range with X-ray free-electron lasers (XFELs) at the Pohang Accelerator Laboratory XFEL (PAL-XFEL) are described. Femtosecond TR-XAS measurements were conducted at the Ru L3-edge of well known photosensitizer tris(bipyridine)ruthenium(II) chloride ([Ru(bpy)3]2+) in water. The results indicate ultrafast photoinduced electron transfer from the Ru center to the ligand, which demonstrates that the newly designed setup is applicable for monitoring ultrafast reactions in the femtosecond domain.

Septum magnet design for compact storage ring

Compact storage rings have been recently constructed or are under construction for industrial or medical applications. Such compact rings operate at tens to hundreds MeV and their footprint is of the order of few meters. Since the size is a critical issue for many applications, the accelerator components installation is extremely dense. Beam injection into such a ring, therefore, takes place with a large bending angle. PAL-EUV is a 400 MeV synchrotron under construction at Pohang Accelerator Laboratory for semiconductor industries. The PAL-EUV accelerator consists of a 20 MeV injector linac, a booster ring and a 400 MeV storage ring, installed in a 15 m by 15 m area enclosed by a concrete wall. Three Lambertson septum magnets are used for the electron injection and extraction between the injector linac, the booster ring and the storage ring. The injection septum in the booster ring bends a 20 MeV electron beam transferred from the injector linac by 60°. The septum magnets for booster ring extraction and storage ring injection bend a 400 MeV beam by 30°. Due to the large bending angle of the septum magnets, the holes for the circulating beams extend to the outer side of the return yokes. In addition, the 2 mm septum thickness for the three septa is a concern for the leakage of the magnetic field which may generate higher order field multipoles in the field-free region of the circulating beam. In this article, we discuss the leakage fields in the septum magnets and how to minimize the impact on the circulating electron beams in the rings.

Comparison of photon beam characteristics of Korea-4GSR with PLS-II

The Korea fourth-generation storage ring (Korea-4GSR), with 4-GeV beam energy and 58-pm-rad emittance has been designed by the Pohang Accelerator Laboratory. The evaluated brilliance and coherence are approximately 100 times higher in the hard X-ray region in Korea-4GSR than in the third-generation storage ring at PLS-II. The coherence properties and preservation of coherence through beamline optical elements were studied using SPECTRA code and hybrid method. Result of this paper show essential information for planning experiments and designing beamlines using ultimate low emittance storage ring.

Measurements of natCd(γ, x) reaction cross sections and isomer ratio of 115m,gCd with the bremsstrahlung end-point energies of 50 and 60 MeV * *Supported by the National Research Foundation of Korea (NRF) through a grant provided by the Ministry of Science and ICT (NRF-2017R1D1A1B03030484, NRF-2013M7A1A1075764, NRF-2018R1A6A1A06024970)

The flux-weighted average cross sections of natCd(γ, xn)115g,m,111m,109,107,105,104Cd and natCd(γ, x)113g,112,111g,110mAg reactions were measured at the bremsstrahlung end-point energies of 50 and 60 MeV. The activation and off-line γ-ray spectrometric technique was carried out using the 100 MeV electron linear accelerator at the Pohang Accelerator Laboratory, Korea. The natCd(γ, xn) reaction cross sections as a function of photon energy were theoretically calculated using the TALYS-1.95 and the EMPIRE-3.2 Malta codes. Then, the flux-weighted average cross sections were obtained from the theoretical values of mono-energetic photons. These values were compared with the flux-weighted values from the present study and were found to be in general agreement. The measured experimental reaction cross-sections and integral yields were described for cadmium and silver isotopes in the natCd(γ, xn)115g,m,111m,109,107,105,104Cd and natCd(γ, x)113g,112,111g,110mAg reactions. The isomeric yield ratio (IR) of 115g,mCd in the natCd(γ, xn) reaction was determined for the two bremsstrahlung end-point energies. The measured isomeric yield ratios of 115g,mCd in the natCd(γ, xn) reaction were also compared with the theoretical values of the nuclear model codes and previously published literature data of the 116Cd(γ, n) and 116Cd(n, 2n) reactions. It was found that the IR value increases with increasing projectile energy, which demonstrates the characteristic of excitation energy. However, the higher IR value of 115g,mCd in the 116Cd(n, 2n) reaction compared to that in the 116Cd(γ, n) reaction indicates the role of compound nuclear spin alongside excitation energy.