Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Yun, Ji-Hye,Li, Xuanxuan,Park, Jae-Hyun,Wang, Yang,Ohki, Mio,Jin, Zeyu,Lee, Wonbin,Park, Sam-Yong,Hu, Hao,Li, Chufeng,Zatsepin, Nadia,Hunter, Mark S.,Sierra, Raymond G.,Koralek, Jake,Yoon, Chun Hong,C American Society for Biochemistry and Molecular Bi 2019 The Journal of biological chemistry Vol.294 No.3

<P>Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all-<I>trans</I> retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.</P>

Hard X-ray von Hamos Spectrometer for Single-Pulse Emission Spectroscopy

Muhammad Ijaz Anwar,Sung Soo Ha,Byung-Jun Hwang,Seonghyun Han,Maverick S. H. Oh,Mohd Faiyaz,Do Young Noh,Hyon Chol Kang,Sunam Kim 한국물리학회 2019 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.75 No.7

We developed a hard X-ray spectrometer for the purpose of measuring X-ray emission spectrum excited by using single X-ray free electron laser (XFEL) pulses. A highly oriented pyrolytic graphite (HOPG) crystal was placed in the von Hamos geometry to focus X-rays of the equal energy on a specific point in detector plane. The spectrometer was tested at PAL-XFEL using Ni and NiO films. The Ni $K_{\beta_{13}}$ X-ray emission line excited by using a single X-ray pulse was successfully resolved. If the much weaker Ni $K_{\beta_{25}}$line is to be observed, data must be accumulated with a few thousands of X-ray pulses. The spectrometer energy resolving power, E/$\Delta E$, was estimated to be 7500. This spectrometer can be utilized to conduct various X-ray emission and absorption measurements using XFELs.

FEL Simulation of New Hard X-ray Undulator Line at PAL-XFEL

Shim Chi Hyun,Kang Heung-Sik 한국물리학회 2020 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.77 No.5

The Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL) has been successfully operating as a remarkably-stable XFEL facility in the world. The hard X-ray beamline, however, has only one undulator line (HX1) with a 26-mm undulator period for which the maximum undulator parameter K is 1.87. The lowest photon energy that can be generated from the HX1 with a maximum electron beam energy at PAL-XFEL (10.5 GeV) is about 14.65 keV. When a lower photon energy than that is required by the beamline users, the electron beam energy has to be decreased, which results in a decreased accessible FEL pulse energy. Therefore, a new hard X-ray undulator line (HX2) with a higher undulator parameter K is needed to make full use of the PAL-XFEL performance in the lower photon energies by increasing the resonant electron beam energy. The undulator period of the HX2 is decided as 35 mm by using Ming Xie's fitting formula to estimate the performance of the HX2. FEL simulations with the GENESIS code are carried out to evaluate the performance of the HX2, including the effect of the post-saturation region. The undulator tapering configuration is optimized by maximizing the FEL intensity for each case. We show that the radiation power at the end of the HX2 can be increased up to 2.5 times higher than that of the HX1 over the entire target photon-energy range of the HX2 (2 ~ 10 keV) by utilizing an undulator with a longer period and a higher undulator parameter K.

Data center of PAL-XFEL

Shin Hocheol,Perazzo Amedeo 한국물리학회 2023 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.82 No.10

A data center is indispensable to experimental light source facilities to provide scientists with both real-time and ofine computing capabilities to analyze, store, and archive the data generated at the beamlines. This paper describes the Pohang Accelerator Laboratory (PAL) computing facility built to support the X-ray Free Electron Laser (XFEL). PAL designed the data center for its XFEL in 2014 and built it in 2015. Some components of the design were driven by lessons learned at the Linac Coherent Light Source (LCLS) XFEL at the SLAC National Accelerator Laboratory. The data center has evolved through three iterations since 2015 and PAL is now planning a fourth upgrade. The storage capacity has increased from 200 TB in 2015 to 1.3 PB in 2019, and 6.9 PB in 2022. On the other hand, PAL has not added servers for computing nodes since the frst deployment. PAL plans to add a new 15 PB storage system and a 30 PB tape library as well as servers for computing nodes and basic services after 2024.

Radiation Size and Divergence at the Hard X-ray Beamline in the PAL-XFEL

박용운,한장희,강흥식,김일남,양해룡,황일문,심치현,고인수 한국물리학회 2014 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.64 No.7

In the Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL), recently, theminimum gap of the hard X-ray undulator were changed from 7.2 (undulator period: 24.4 mm)to 8.3 mm (undulator period: 26 mm). To review the physical issues related to the gap change,including the radiation size and divergence, in the PAL-XFEL, we did a simulation study withGENESIS 1.3. The saturation length in the 8.3-mm case will be increased by 10% with respectto the 7.2-mm case. The study also revealed that the divergence of the radiation in 8.3-mm casewould be decreased by 4% compared with that in the 7.2-mm case. In this paper, we will presentthe detailed simulation results to estimate the divergence of radiation at the hard X-ray beamlinein the PAL-XFEL.

Data Acquisition System of Multi-Port Charge-Coupled Device for PAL-XFEL

박상윤,박기수,현효정,김경숙 한국물리학회 2019 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.75 No.1

After first lasing on 14 June 2016 of X-ray Free Electron Laser facility at Pohang Accelerator Laboratory (PAL-XFEL), various experiments using hard X-ray have been done using Multi-Port Charge-Coupled Device detector (MPCCD). To achieve time-resolved analysis, either the timestamp or pulse-ID tagging to the data generated from detectors is a key ingredient. For this we established the hardware interfaces including MPCCD software to synchronize PAL-XFEL event timing system. In this paper, the developed data acquisition system (DAQ) of the MPCCD is introduced including the event timing system and timestamp or pulse-ID, and the data frameworks of the PAL-XFEL.

High-power Test of the New 3-dB Power Splitter for the PAL XFEL S-band LINAC RF System

주영도,박용정,허훈,Jinyul Hu,Sung-Soo Park,이상희,황운하,Gun-Young Moon,Sosung Lee,이흥수 한국물리학회 2014 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.64 No.8

The 3-dB power splitter to be used in the Pohang Accelerator Laboratory X-ay Free-electronLaser (PAL XFEL), which have been under construction since 2011, must operate at a peak powerof 400 MW and a repetition rate of 120 Hz. For these operational conditions of the PAL XFEL,the old 3-dB power splitter that was originally designed to be used in the PLS LINAC will mostsuffer from RF breakdown. Therefore, for the new 3-dB power splitter, the original design hasbeen modified to reduce the field gradient and the surface current. The new 3-dB power splitteris designed by using a finite-difference time-domain (FDTD) simulation. We have fabricated aprototype, and the result of a high-power test indicates that the RF performance of the new 3-dBpower splitter satisfies the specifications of the PAL XFEL S-band LINAC RF system.

Stability Issues of RF System for PAL XFEL

J. S. Oh,W. H. Hwang,S. S. Park,S. H. Kim,Y. J. Han,S. D. Jang,Y. G. Son,S. J. Kwon,J. H. Suh 한국물리학회 2009 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.54 No.1

The PAL (Pohang Accelerator Laboratory) is persuading to build an X-ray FEL (free electron laser) facility (PAL XFEL), of which the stable electron beam is essential. The beam energy stability is governed by an accelerating RF eld. The stable charging power supply is mostly responsible to the stable RF eld. Therefore, we are developing ultra stable klystron modulators. In addition, the slow drift of RF phase due to the thermal eect is to be compensated by a phase feedback system. This paper shows on-going R&Ds for two types of stability improvement schemes and a phase feedback system. The PAL (Pohang Accelerator Laboratory) is persuading to build an X-ray FEL (free electron laser) facility (PAL XFEL), of which the stable electron beam is essential. The beam energy stability is governed by an accelerating RF eld. The stable charging power supply is mostly responsible to the stable RF eld. Therefore, we are developing ultra stable klystron modulators. In addition, the slow drift of RF phase due to the thermal eect is to be compensated by a phase feedback system. This paper shows on-going R&Ds for two types of stability improvement schemes and a phase feedback system.

Parameter Optimization of PAL-XFEL Injector

이재현,고인수,한장희,홍주호,양해룡,민창기,강흥식 한국물리학회 2018 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.72 No.10

A photoinjector is used as the electron source to generate a high peak current and low emittance beam for an X-ray free electron laser (FEL). The beam emittance is one of the critical parameters to determine the FEL performance together with the slice energy spread and the peak current. The Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL) was constructed in 2015, and the beam commissioning was carried out in spring 2016. The injector is running routinely for PAL-XFEL user operation. The operational parameters of the injector have been optimized experimentally, and these are somewhat different from the originally designed ones. Therefore, we study numerically the injector parameters based on the empirically optimized parameters and review the present operating condition.

S-band Accelerating Structures for the PAL-XFEL

이흥수,박영정,주영도,허훈,허진열,김상희,박성수,황운하,강흥식,김광우,고인수,오경민,노성주,박용환,Hiroshi Matsumoto 한국물리학회 2015 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.66 No.3

One hundred seventy-two accelerating structures are required for the Pohang Accelerator LaboratoryX-ray free-electron laser’s (PAL-XFEL’s) 10-GeV main linear accelerator. So far, we havepurchased 80 structures from Mitsubishi Heavy Industry (MHI), which have quasi-symmetric couplersin the accelerating structure to reduce the quadruple and the sextuple components of theelectric field in the coupling cavity. High-power tests have been conducted for the first structure ofthe MHI structure, and Research Instruments (RI) has developed a 3-m long accelerating structurethat has an operating frequency of 2856 MHz and in/out couplers of quasi-symmetric racetrackshape for the PAL-XFEL linear accelerator. This structure also has been tested by PAL and RIin the Pohang accelerator laboratory (PAL) to check the maximum available electric field gradient. We will describe the test results of these structures and the current status for the fabrication of theother accelerating structures in this paper.