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At least 19 records

Data Analysis using Psocake at PAL-XFEL

Psocake is a software program designed for high throughput data reduction and analysis of free-electron laser experiments. Its serial crystallography graphical user interface allows browsing of detector images, Bragg peak finding with easy parameter tuning, generate region-of-interest masks, and crystal indexing. It was originally developed for use at the Linac Coherent Light Source, SLAC national accelerator laboratory and has been adopted for use at Pohang accelerator laboratory due to popular demand. Here, we describe the features of psocake available at Pohang and include information about data management that we hope will be useful for users of the facility.

43 PARTICLE ACCELERATORS↗

Design of Monolithic Bi-Layer High-Z PAL-Si Hard X-ray CMOS Image Sensors for Quantum Efficiency Enhancement

This article experimentally investigates the inception of an innovative hard X-ray photon energy attenuation layer (PAL) to advance high-energy X-ray detection (20–50 keV). A bi-layer design with a thin film high-Z PAL on the top and Si image sensor on the bottom has previously demon-strated quantum yield enhancement via computational methods by the principle of photon energy down conversion (PEDC), where high-energy X-ray photon energies are attenuated via inelastic scattering down to ≤10 keV, which is suitable for efficient photoelectric absorption by Si. Quantum yield enhancement has been experimentally confirmed via a preliminary demonstration using PAL-integrated Si-based CMOS image sensors (Si CIS). Furthermore, substituting the high-Z PAL with a lower-Z material—Sn—and alternatively coupling it with a conventional scintillator ma-terial—Lutetium-yttrium oxyorthosilicate (LYSO)—have been compared to demonstrate the most prominent efficacy of monolithic integration of high-Z PAL on Si CIS to detect hard X-rays, paving the way for next-generation high-energy X-ray detection methods.

47 OTHER INSTRUMENTATION↗

Candidate members of the Pal 5, GD-1, Cetus Polar and Orphan tidal stellar halo streams from SDSS DR9, LAMOST DR3 and APOGEE catalogs

We present candidate members of the Pal 5, GD-1, Cetus Polar, and Orphan tidal stellar streams found in LAMOST DR3, SDSS DR9 and APOGEE catalogs. In LAMOST DR3, we find 20, 4, 24 high confidence candidates of tidal streams GD-1, Cetus Polar and Orphan respectively. We also list from the SDSS DR9 spectroscopic catalog 59, 118, 10 high confidence candidates of tidal streams Cetus Polar, Orphan and Pal 5, respectively. Furthermore, we find 7 high confidence candidates of the Pal 5 tidal stream in APOGEE data. Compared with SDSS, the new candidates from LAMOST DR3 are brighter, so that together, more of the color-magnitude diagram, including the giant branch can be explored. Analysis of SDSS data shows that there are 3 metallicity peaks of the Orphan stream and also shows some spatial separation. LAMOST data confirms multiple metallicities in this stream. The metallicity, given by the higher resolution APOGEE instrument, of the Pal 5 tidal stream is [Fe/H] $\sim -1.2$, higher than that given earlier by SDSS spectra. Here, many previously unidentified stream members are tabulated here for the first time, along with existing members, allowing future researchers to further constrain the orbits of these objects as they move within the Galaxy's dark matter potential.

79 ASTRONOMY AND ASTROPHYSICS↗

Investigation of the damping wiggler effect and application on the PAL fourth-generation storage ring

An investigation of the damping wiggler effect to reduce the emittance in the Pohang Accelerator Laboratory (PAL), a fourth-generation storage ring (4GSR) that uses a multi-bend achromat, is presented. Furthermore, a 4GSR lattice which has reduced emittance and increased dynamic aperture to amplify the synergy with two existing light sources (PLS-II and PAL-XFEL) at PAL is described.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

PALS Python v0.1.0

This is a Python implementation for the Particle Accelerator Lattice Standard (PALS). To define the PALS schema, Pydantic is used to map to Python objects, perform automatic validation, and serialize/deserialize data classes to/from many modern file formats. Various modern file formats (e.g., YAML, JSON, TOML, XML, etc.) are supported, which makes the implementation of the schema-following files in any modern programming language easy (e.g., Python, Julia, C++, LUA, Javascript, etc.). Here, we do Python.

Huebl, Axel [Lawrence Berkeley National Laboratory↗

Progress in the development of the community Particle Accelerator Lattice Standard (PALS)

The Particle Accelerator Lattice Standard (PALS) is a community effort to create an open standard to promote lattice information exchange for particle accelerators. PALS development is a community-wide international effort involving accelerator physicists from multiple institutions. While it started as a lattice standard for beam dynamics simulations, it is now being extended to support other particle accelerator activities, in particular accelerator operation. With new accelerators that are becoming more complex, larger collaborations and the increasing imprint of artificial intelligence in all accelerator activities (from design to operation to workforce development), the imperative for a common, standardized accelerator ontology has been transitioning from “nice-to-have” to “must-have”. We will present the status of the project, its relations to other projects, including to two of the particle accelerator projects of the newly announced US DOE Genesis Mission: the Multi-Office Accelerator Team (MOAT) project and the Nuclear physics AI-Ready Accelerator Data (NARAD) project.

Brynes, A. [Science and Technology Facilities Coun↗

The shape of the inner Milky Way halo from observations of the Pal 5 and GD-1 stellar streams

We constrain the shape of the Milky Way’s halo by dynamical modeling of the observed phase-space tracks of the Pal 5 and GD–1 tidal streams. We find that the only information about the potential gleaned from the tracks of these streams are precise measurements of the shape of the gravitational potential—the ratio of vertical to radial acceleration—at the location of the streams, with weaker constraints on the radial and vertical accelerations separately. The latter will improve significantly with precise proper-motion measurements from Gaia. We measure that the overall potential flattening is 0.95 ± 0.04 at the location of GD–1 ([R,Z]≈[12.5,6.7] kpc) and 0.94 ± 0.05 at the position of Pal 5 ([R,Z]≈[8.4,16.8] kpc). Combined with constraints on the force field near the Galactic disk, we determine that the axis ratio of the dark-matter halo’s density distribution is 1.05 ± 0.14 within the inner 20 kpc, with a hint that the halo becomes more flattened near the edge of this volume. The halo mass within 20 kpc is (1.1±0.1)×10{sup 11} M{sub ⊙}. A dark-matter halo this close to spherical is in tension with the predictions from numerical simulations of the formation of dark-matter halos.

79 ASTRONOMY AND ASTROPHYSICS↗

Glucosinolate and phenylpropanoid biosynthesis are linked by proteasome-dependent degradation of PAL

Plants produce several hundreds of thousands of secondary metabolites that are important for adaptation to various environmental conditions. Although different groups of secondary metabolites are synthesized through unique biosynthetic pathways, plants must orchestrate their production simultaneously. Phenylpropanoids and glucosinolates are two classes of secondary metabolites that are synthesized through apparently independent biosynthetic pathways. Genetic evidence has revealed that the accumulation of glucosinolate intermediates limits phenylpropanoid production in a Mediator Subunit 5 (MED5)-dependent manner. To elucidate the molecular mechanism underlying this process, here we analyzed the transcriptomes of a suite of Arabidopsis thaliana glucosinolate-deficient mutants using RNAseq and identified misregulated genes that are rescued by the disruption of MED5. The expression of a group of Kelch Domain F-Box genes (KFBs) that function in PAL degradation is affected in glucosinolate biosynthesis mutants and the disruption of these KFBs restores phenylpropanoid deficiency in the mutants. Our study suggests that glucosinolate/phenylpropanoid metabolic crosstalk involves the transcriptional regulation of KFB genes that initiate the degradation of the enzyme phenylalanine ammonia-lyase, which catalyzes the first step of the phenylpropanoid biosynthesis pathway. Nevertheless, KFB mutant plants remain partially sensitive to glucosinolate pathway mutations, suggesting that other mechanisms that link the two pathways also exist.

59 BASIC BIOLOGICAL SCIENCES↗

AI-Ready Semantic Infrastructure for CEBAF: From CED to PALS Knowledge Graphs

JLab and PNNL are jointly developing an AI-ready data ecosystem that exposes the Continuous Electron Beam Acceleration Facility’s (CEBAF’s) operational configuration, lattice description, and control-system channels to agentic optimization frameworks through a standards-based semantic layer. The effort integrates the existing facility-specific CEBAF Element Database (CED) with extensions of the emerging facility-agnostic Particle Accelerator Lattice Standard (PALS) to produce a knowledge graph (KG) containing coherent, machine-interpretable views of devices, signals, and regions. With this KG, CEBAF’s setpoints, readbacks, and device hierarchies become queryable using a uniform declarative graph query language (e.g., Neo4j Cypher), providing intents and inspectable semantics suitable for agentic control. The resulting graph-backed interfaces will allow autonomous agents to retrieve authoritative machine configurations, reason over device- and signal-level relationships, and execute tuning and diagnostic workflows without bespoke CEBAF-specific logic, thereby delivering a scalable pathway from operational data to trustworthy agentic accelerator tuning frameworks.

Zhang, He [Thomas Jefferson National Accelerator F↗

Hard X-ray self-seeding commissioning at PAL-XFEL

A wake monochromator based on a large-area diamond single crystal for hard X-ray self-seeding has been successfully installed and commissioned in the hard X-ray free-electron laser (FEL) at the Pohang Accelerator Laboratory with international collaboration. For this commissioning, the self-seeding was demonstrated with a low bunch charge (40 pC) and the nominal bunch charge (180 pC) of self-amplified spontaneous emission (SASE) operation. The FEL pulse lengths were estimated as 7 fs and 29.5 fs, respectively. In both cases, the average spectral brightness increased by more than three times compared with the SASE mode. The self-seeding experiment was demonstrated for the first time using a crystal with a thickness of 30 µm, and a narrow bandwidth of 0.22 eV (full width at half-maximum) was obtained at 8.3 keV, which confirmed the functionality of a crystal with such a small thickness. In the nominal bunch-charge self-seeding experiment, the histogram of the intensity integrated over a 1 eV bandwidth showed a well defined Gaussian profile, which is evidence of the saturated FEL and a minimal electron-energy jitter (~1.2 × 10 –4 ) effect. Here, the corresponding low photon-energy jitter (~2.4 × 10 –4 ) of the SASE FEL pulse, which is two times lower than the Pierce parameter, enabled the seeding power to be maximized by maintaining the spectral overlap between SASE FEL gain and the monochromator.

47 OTHER INSTRUMENTATION↗

Brachypodium Phenylalanine Ammonia Lyase (PAL) Promotes Antiviral Defenses against Panicum mosaic virus and Its Satellites

Brachypodium distachyon has recently emerged as a premier model plant for monocot biology, akin to Arabidopsis thaliana. We previously reported genome-wide transcriptomic and alternative splicing changes occurring in Brachypodium during compatible infections with Panicum mosaic virus (PMV) and its satellite virus (SPMV). Here, we dissected the role of Brachypodium phenylalanine ammonia lyase 1 (PAL1), a key enzyme for phenylpropanoid and salicylic acid (SA) biosynthesis and the induction of plant defenses. Targeted metabolomics profiling of PMV-infected and PMV- plus SPMV-infected (PMV/SPMV) Brachypodium plants revealed enhanced levels of multiple defense-related hormones and metabolites such as cinnamic acid, SA, and fatty acids and lignin precursors during disease progression. The virus-induced accumulation of SA and lignin was significantly suppressed upon knockdown of B. distachyon PAL1 (BdPAL1) using RNA interference (RNAi). The compromised SA accumulation in PMV/SPMV-infected BdPAL1 RNAi plants correlated with weaker induction of multiple SA-related defense gene markers (pathogenesis related 1 [PR-1], PR-3, PR-5, and WRKY75) and enhanced susceptibility to PMV/SPMV compared to that of wild-type (WT) plants. Furthermore, exogenous application of SA alleviated the PMV/SPMV necrotic disease phenotypes and delayed plant death caused by single and mixed infections. Together, our results support an antiviral role for BdPAL1 during compatible host-virus interaction, perhaps as a last resort attempt to rescue the infected plant.

59 BASIC BIOLOGICAL SCIENCES↗

PAL Experimental Report Form

We constructed the first simultaneous dark- and bright-field X-ray microscope in this experiment, coupling it to simultaneous measurements of the wide-angle Xray diffraction, and the XFEL pulse intensity and energy spectrum on each shot. This experiment established proof of concept for this new advanced measurement technique and demonstrated DFXM at an XFEL for the first time. Within this complex experiment, we also acquired data that advanced our research goals within materials science and mathematics. These included: A preliminary study of how local effects reduce the X-ray damage threshold in diamond; A preliminary study of how X-ray radiation imparts heat into materials based on irreversible phase transitions that occur in boric acid with increasing temperature (based on hydration); A study of X-ray radiation damage from ultrafast thermal cycling and nonthermal melting in bismuth selenide; We also began developing software to automate alignment of compound refractive lenses (CRLs) using stochastic Nelder-Mead optimization methods. This work will expedite and improve the accuracy of alignments for many future experiments using CRLs.

36 MATERIALS SCIENCE↗