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Student-Friendly Guide to Molecular Integrals

Preceding even the Hartree–Fock method, molecular integrals are the very foundation upon which quantum chemical molecular modeling depends. Discussions of molecular integrals are normally found only in advanced and technical texts or articles. The objective of the present article is to provide less experienced readers, or students in a physical/computational chemistry course, a thorough understanding of molecular integrals. Through a series of detailed Handouts, the student/reader can participate in the derivation of molecular integrals, and in turn implement them in computer code. Hartree–Fock theory is discussed in enough detail to motivate the molecular integrals and address such topics as the atomic orbital basis. An introduction to the programming language of choice, Python3, is provided, tailored toward developing the essential skills necessary for implementing molecular integrals. In conclusion, the article is intended to be useful not only to instructors of physical/computational chemistry, but also to any reader who has independently sought a primer on this elusive subject.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An approach to developing an integrated pyroprocessing simulator

Pyroprocessing has been studied for a decade as one of the promising fuel recycling options in Korea. We have built a pyroprocessing integrated inactive demonstration facility (PRIDE) to assess the feasibility of integrated pyroprocessing technology and scale-up issues of the processing equipment. Even though such facility cannot be replaced with a real integrated facility using spent nuclear fuel (SF), many insights can be obtained in terms of the world's largest integrated pyroprocessing operation. In order to complement or overcome such limited test-based research, a pyroprocessing Modelling and simulation study began in 2011. The Korea Atomic Energy Research Institute (KAERI) suggested a Modelling architecture for the development of a multi-purpose pyroprocessing simulator consisting of three-tiered models: unit process, operation, and plant-level-model. The unit process model can be addressed using governing equations or empirical equations as a continuous system (CS). In contrast, the operation model describes the operational behaviors as a discrete event system (DES). The plant-level model is an integrated model of the unit process and an operation model with various analysis modules. An interface with different systems, the incorporation of different codes, a process-centered database design, and a dynamic material flow are discussed as necessary components for building a framework of the plant-level model. As a sample model that contains methods decoding the above engineering issues was thoroughly reviewed, the architecture for building the plant-level-model was verified. By analyzing a process and operation-combined model, we showed that the suggested approach is effective for comprehensively understanding an integrated dynamic material flow. This paper addressed the current status of the pyroprocessing Modelling and simulation activity at KAERI, and also predicted its path forward.

42 ENGINEERING↗

Self-consistent integrated modeling of combined hybrid discharge-laser produced plasma devices for extreme ultraviolet metrology

Discharge- and laser-produced plasma (DLPP) devices are being used as light sources for extreme ultraviolet (EUV) generation. A key challenge for both, DPP and LPP, is achieving sufficient brightness to support the throughput requirements of nanometrology tools. To simulate the environment of a hybrid DLPP device and optimize the EUV output, we have developed an integrated HEIGHTS-DLPP computer simulation package. The package integrates simulation of two evolving plasmas (DPP and LPP) and includes modeling of a set of integrated self-consistent processes: external power source and plasma energy balance, plasma resistive magnetohydrodynamics, plasma heat conduction, detailed radiation transport (RT), and laser absorption and refraction. We simulated and optimized DLPP devices using Xe gas as a target material. We synchronized the external circuit parameters, chamber gas parameters, and laser beam temporal and spatial profiles to achieve maximum EUV output. The full 3D Monte Carlo scheme was integrated for detailed RT and EUV output calculations in Xe using more than 3600 spectral groups. The modeling results are in good agreement with Julich Forschungszentrum experimental data. Theoretical models, developed and integrated into the HEIGHTS package, showed wide capabilities and flexibility. In conclusion, the models and package can be used for optimization of the experimental parameters and settings, investigation of DLPP devices with complex design, analyzing the impact of integrated spatial effects and working timeline arrangement on the final EUV output, and EUV source size, shape, and angular distribution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Flexible, integrated modeling of tokamak stability, transport, equilibrium, and pedestal physics

The STEP (Stability, Transport, Equilibrium, and Pedestal) integrated-modeling tool has been developed in OMFIT to predict stable, tokamak equilibria self-consistently with core-transport and pedestal calculations. STEP couples theory-based codes to integrate a variety of physics, including magnetohydrodynamic stability, transport, equilibrium, pedestal formation, and current-drive, heating, and fueling. The input/output of each code is interfaced with a centralized ITER-Integrated Modelling & Analysis Suite data structure, allowing codes to be run in any order and enabling open-loop, feedback, and optimization workflows. This paradigm simplifies the integration of new codes, making STEP highly extensible. STEP has been verified against a published benchmark of six different integrated models. Core-pedestal calculations with STEP have been successfully validated against individual DIII-D H-mode discharges and across more than 500 discharges of the H98,y2 database, with a mean error in confinement time from experiment less than 19%. STEP has also reproduced results in less conventional DIII-D scenarios, including negative-central-shear and negative-triangularity plasmas. Predictive STEP modeling has been used to assess performance in several tokamak reactors. Simulations of a high-field, large-aspect-ratio reactor show significantly lower fusion power than predicted by a zero-dimensional study, demonstrating the limitations of scaling-law extrapolations. STEP predictions have found promising scenarios for an EXhaust and Confinement Integration Tokamak Experiment, including a high-pressure, 80%-bootstrap-fraction plasma. ITER modeling with STEP has shown that pellet fueling enhances fusion gain in both the baseline and advanced-inductive scenarios. Finally, STEP predictions for the SPARC baseline scenario are in good agreement with published results from the physics basis.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Optimizing time integration for accurate recovery of shockwave interface location in radiography

We present simulations and experiments of time integrated radiographic imaging of a moving 1D shock wave front and a quantitative method for determining the statistical error in locating the shock front as a function of integration time and noise in the radiograph. We discuss the trade-off between increasing motion blur, which leads to decreased shock front location certainty, and increasing signal-to-noise, which leads to improved image quality with increasing integration time. We find an optimum integration time between a short integration time, where noise limits the error, and a long integration time, where motion blurring limits the error. This methodology can be used to tune experimental configurations to obtain the highest quality radiograph for a given experimental configuration.

Bremsstrahlung↗

Emergent local integrals of motion without a complete set of localized eigenstates

Systems where all energy eigenstates are localized are known to display an emergent local integrability, in the sense that one can construct an extensive number of operators that commute with the Hamiltonian and are localized in real space. Here we show that emergent local integrability does not require a set of localized eigenstates to be complete. Given a set of localized eigenstates comprising a nonzero fraction (1 - pf) of the full many-body spectrum, one can construct an extensive number of integrals of motion which are local in the sense that they have nonzero weight in a compact region of real space, in the thermodynamic limit. However, these modified integrals of motion have a “global dressing” whose weight vanishes as ~pf as pf → 0. In this sense, the existence of a nonzero fraction of localized eigenstates is sufficient for emergent local integrability. We discuss the implications of our findings for systems where the spectrum contains delocalized states, for systems with projected Hilbert spaces, and for the robustness of quantum integrability.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Integrable symplectic maps with a polygon tessellation

Identifying integrable dynamics remains a formidable challenge, and despite centuries of research, only a handful of examples are known to date. In this article, we explore a distinct form of area-preserving (symplectic) mappings derived from the stroboscopic Poincaré cross section of a kicked rotator—an oscillator subjected to an external force periodically switched on in short pulses. The significance of this class of problems extends to various applications in physics and mathematics, including particle accelerators, crystallography, and studies of chaos. Notably, Suris's theorem constrains the integrability within this category of mappings, outlining potential scenarios with analytic invariants of motion. In this paper, we challenge the assumption of the analyticity of the invariant by exploring piecewise linear transformations on a torus ( T 2 ) and associated systems on the plane ( R 2 ), incorporating arithmetic quasiperiodicity and discontinuities. Introducing a new automated technique, we discovered previously unknown scenarios featuring polygonal invariants that form perfect tessellations and, moreover, fibrations of the plane or torus. This work reveals a novel category of planar tilings characterized by discrete symmetries that emerge from the invertibility of transformations and are intrinsically linked to the presence of integrability. Our algorithm relies on the analysis of the Poincaré rotation number and its piecewise monotonic nature for integrable cases, contrasting with the noisy behavior in the case of chaos, thereby allowing for clear separation. Some of the newly discovered systems exhibit the peculiar behavior of “integrable diffusion,” characterized by infinite and quasirandom hopping between tiles while being confined to a set of invariant segments. Finally, through the implementation of a smoothening procedure, all mappings can be generalized to quasi-integrable scenarios with suppressed volume occupied by chaotic trajectories, thereby opening doors to potential practical applications. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗

Development of an Integrated Electro-Hydraulic Machine to Electrify Off-highway Vehicles

Electrification of off-highway vehicles is notoriously challenging due to extreme power density requirements. This paper proposes and develops an axial flux machine integrated with a hydraulic pump to realize a single modular, electro-hydraulic machine to electrify off-highway vehicle implements. This integrated machine eliminates redundant bearings, couplings, and shaft seals, re-uses surfaces, and enables direct cooling of the electric machine with the hydraulic fluid, to significantly increase power density. Three popular axial flux machine variants are first compared using an FEA-based design optimization approach. The single rotor, single stator variant is identified to be the most promising for integration with the hydraulic pump. Next, a multi-physics framework of the complete integrated hydraulic pump and axial flux machine is developed to characterize the design space. The results indicate promising potential for this concept to realize efficiency over 85% and power density over 5kW/kg for the complete machine (electric machine, hydraulic pump, and thermal management system), while utilizing conventional materials (thin gauge silicon steel, N45 magnets, and enamelled copper wire). Furthermore, a prototype axial flux machine has been experimentally characterized and integrated with a hydraulic pump to demonstrate the integrated electro-hydraulic machine concept.

33 ADVANCED PROPULSION SYSTEMS↗

Renewable Integration in Hybrid ac-dc Systems using Multi-port Autonomous Reconfigurable Solar power plant (MARS)

To increase inertia and improve primary frequency response of future grids, grid-forming inverters connecting PV to grid and energy storage systems (ESSs) are likely to play an important role. Moreover, high-voltage direct current (HVdc) links will also be an enabler to transfer remote PV generation and for improved grid stability. That is, with increased penetration of PV, discrete development of PV and ESS connecting to transmission ac grid and HVdc links is one of the solutions for stable operation of grid. Here, an integrated concept for integration of PV and ESS to transmission ac grid and HVdc links is proposed that is named as multi-port autonomous reconfigurable solar power plant (MARS). The proposed integrated development reduces the cost associated with respect to discrete development of PV-ESS systems connecting to transmission ac grid and HVdc links. The integrated development incorporates advanced control methods to provide inertial and primary frequency response, reactive power support, and transient stability to manage PV and ESS resources. In this paper, high-fidelity switched system model of the integrated system and grids are developed and detailed simulation results are provided to showcase the stable operation of the integrated system and provision of grid support functions.

14 SOLAR ENERGY↗

Integrating Empirical-Modeling Approaches to Improve Understanding of Terrestrial Ecology Processes

Recent decades have seen tremendous increases in the quantity of empirical ecological data collected by individual investigators, as well as through research networks such as FLUXNET (Baldocchi et al., 2001). At the same time, advances in computer technology have facilitated the development and implementation of large and complex land surface and ecological process models. Separately, each of these information streams provides useful, but imperfect information about ecosystems. To develop the best scientific understanding of ecological processes, and most accurately predict how ecosystems may cope with global change, integration of empirical and modeling approaches is necessary. However, true integration - in which models inform empirical research, which in turn informs models (Fig. 1) - is not yet common in ecological research (Luo et al., 2011). The goal of this workshop, sponsored by the Department of Energy, Office of Science, Biological and Environmental Research (BER) program, was to bring together members of the empirical and modeling communities to exchange ideas and discuss scientific practices for increasing empirical - model integration, and to explore infrastructure and/or virtual network needs for institutionalizing empirical - model integration (Yiqi Luo, University of Oklahoma, Norman, OK, USA). The workshop included presentations and small group discussions that covered topics ranging from model-assisted experimental design to data driven modeling (e.g. benchmarking and data assimilation) to infrastructure needs for empirical - model integration. Ultimately, three central questions emerged. How can models be used to inform experiments and observations? How can experimental and observational results be used to inform models? What are effective strategies to promote empirical - model integration?

54 ENVIRONMENTAL SCIENCES↗

Thermal Management System of an Outer-Rotor-Motor-Based Traction Drive With Integrated Power Electronics in its Central Cavity

Increasing power densities of electric vehicle traction drive systems necessitates combining the electric motor and the power electronics into one unit. A compact, integrated traction drive unit with fewer components also drives production costs down, enabling wider adoption of electric vehicles. However, the integration of power electronics in the electric machine is associated with challenges of designing an effective thermal management solution for the combined traction drive system. This paper focuses on the thermal management approach selected for Oak Ridge National Laboratory’s outer-rotor-motor-based integrated traction drive and evaluates its potential performance. The outer-rotor-motor configuration provided an opportunity for integration of the six-phase inverter in the available space in the central cavity of the internal stator. A cylindrical inverter enclosure with integrated coolant (water-ethylene glycol) channels in its walls was designed to enable heat removal from the power electronics. Numerical thermal-fluid modeling and initial channel/fin optimization results for the cylindrical heat sink are presented here. As permanent magnets are integrated in a high-speed (20 000 RPM) outer rotor, forced air convection provides cooling for the magnets. The magnets were segmented axially to mitigate the eddy current losses. Heat generated in the stator windings and laminations is removed by water-ethylene glycol coolant circulating in interpolar T-shape ceramic heat exchangers inserted between windings. General design concepts and numerical thermal-fluid simulations illustrating the electric motor thermal management solution are also presented.

Kekelia, Bidzina↗

Molecular radiotherapy: The NUKFIT software for calculating the time-integrated activity coefficient

Purpose: Calculation of the time-integrated activity coefficient (residence time) is a crucial step in dosimetry for molecular radiotherapy. However, available software is deficient in that it is either not tailored for the use in molecular radiotherapy and/or does not include all required estimation methods. The aim of this work was therefore the development and programming of an algorithm which allows for an objective and reproducible determination of the time-integrated activity coefficient and its standard error.Methods: The algorithm includes the selection of a set of fitting functions from predefined sums of exponentials and the choice of an error model for the used data. To estimate the values of the adjustable parameters an objective function, depending on the data, the parameters of the error model, the fitting function and (if required and available) Bayesian information, is minimized. To increase reproducibility and user-friendliness the starting values are automatically determined using a combination of curve stripping and random search. Visual inspection, the coefficient of determination, the standard error of the fitted parameters, and the correlation matrix are provided to evaluate the quality of the fit. The functions which are most supported by the data are determined using the corrected Akaike information criterion. The time-integrated activity coefficient is estimated by analytically integrating the fitted functions. Its standard error is determined assuming Gaussian error propagation. The software was implemented using MATLAB.Results: To validate the proper implementation of the objective function and the fit functions, the results of NUKFIT and SAAM numerical, a commercially available software tool, were compared. The automatic search for starting values was successfully tested for reproducibility. The quality criteria applied in conjunction with the Akaike information criterion allowed the selection of suitable functions. Function fit parameters and their standard error estimated by using SAAM numerical and NUKFIT showed differences of <1%. The differences for the time-integrated activity coefficients were also <1% (standard error between 0.4% and 3%). In general, the application of the software is user-friendly and the results are mathematically correct and reproducible. An application of NUKFIT is presented for three different clinical examples.Conclusions: The software tool with its underlying methodology can be employed to objectively and reproducibly estimate the time integrated activity coefficient and its standard error for most time activity data in molecular radiotherapy.

61 RADIATION PROTECTION AND DOSIMETRY↗

SU-C-207-07: Quantification of Coronary Artery Cross-Sectional Area in CT Angiography Using Integrated Density: A Phantom Study

Purpose: To investigate the feasibility of quantifying the cross-sectional area (CSA) of coronary arteries using integrated density in a physics-based model with a phantom study. Methods: In this technique the total integrated density of the object as compared with its local background is measured so it is possible to account for the partial volume effect. The proposed method was compared to manual segmentation using CT scans of a 10 cm diameter Lucite cylinder placed inside a chest phantom. Holes with cross-sectional areas from 1.4 to 12.3 mm{sup 2} were drilled into the Lucite and filled with iodine solution, producing a contrast-to-noise ratio of approximately 26. Lucite rods 1.6 mm in diameter were used to simulate plaques. The phantom was imaged with and without the Lucite rods placed in the holes to simulate diseased and normal arteries, respectively. Linear regression analysis was used, and the root-mean-square deviations (RMSD) and errors (RMSE) were computed to assess the precision and accuracy of the measurements. In the case of manual segmentation, two readers independently delineated the lumen in order to quantify the inter-reader variability. Results: The precision and accuracy for the normal vessels using the integrated density technique were 0.32 mm{sup 2} and 0.32 mm{sup 2}, respectively. The corresponding results for the manual segmentation were 0.51 mm{sup 2} and 0.56 mm{sup 2}. In the case of diseased vessels, the precision and accuracy of the integrated density technique were 0.46 mm{sup 2} and 0.55 mm{sup 2}, respectively. The corresponding results for the manual segmentation were 0.75 mm{sup 2} and 0.98 mm{sup 2}. The mean percent difference for the two readers was found to be 8.4%. Conclusion: The CSA based on integrated density had improved precision and accuracy as compared with manual segmentation in a Lucite phantom. The results indicate the potential for using integrated density to improve CSA measurements in CT angiography.

60 APPLIED LIFE SCIENCES↗

SU-E-P-20: Personnel Lead Apparel Integrity Inspection: Where We Are and What We Need?

Purpose: In recent years, tremendous efforts have been devoted to radiation dose reduction, especially for patients who are directly exposed to primary radiation or receive radiopharmaceuticals. Limited efforts have been focused on those personnel who are exposed to secondary radiation while fulfilling their work responsibilities associated with diagnostic imaging and image-guided interventions. Occupational exposure is compounded in daily practice and can lead to a significant radiation dose over time. Personnel lead apparel is a well-accepted engineering control to protect healthcare workers when radiation is inevitable. The question is, do we have a nationally established program to protect personnel? This study is to investigate the lead apparel inspection programs among the USA. Methods: A series of surveys of state regulations, the University Health System Consortium, and federal regulations and regulations determined by accrediting bodies were conducted. The surveys were used to determine the current status of lead apparel programs regarding integrity inspections. Based on the survey results, a thorough program was proposed accordingly. Results: Of 50 states, seventeen states and Washington D.C. require lead apparel integrity inspections within their state regulations. Eleven of these states specify that the inspection is required on an annual basis. Two of these states require lead apron integrity checks to be performed semi-annually. Eleven out of the two hundred academic medical centers surveyed responded. The results show that the method (visually vs. fluoroscopy) used to conduct lead apparel integrity checks differ greatly amongst healthcare organizations. The FDA, EPA, CRCPD and NCRP require lead apparel integrity checks. However, the level of policies is different. A standard program is not well established and clearly there is a lack of standardization. Conclusion: A program led by legislative (state or federal government) and with specific frequency, methods, tracking and criteria is needed to ensure the integrity of personnel lead apparel.

60 APPLIED LIFE SCIENCES↗

SU-E-I-25: Quantification of Coronary Artery Cross-Sectional Area in CT Angiography Using Integrated Density: A Simulation Study

Purpose: To develop a physics-based model for accurate quantification of the cross-sectional area (CSA) of coronary arteries in CT angiography by measuring the integrated density to account for the partial volume effect. Methods: In this technique the integrated density of the object as compared with its local background is measured to account for the partial volume effect. Normal vessels were simulated as circles with diameters in the range of 0.1–3mm. Diseased vessels were simulated as 2, 3, and 4mm diameter vessels with 10–90% area stenosis, created by inserting circular plaques. A simplified two material model was used with the lumen as 8mg/ml Iodine and background as lipid. The contrast-to-noise ratio between lumen and background was approximately 26. Linear fits to the known CSA were calculated. The precision and accuracy of the measurement were quantified using the root-mean-square fit deviations (RMSD) and errors to the known CSA (RMSE). Results compared to manual segmentation of the vessel lumen. To assess the impact of random variations, coefficients of variation (CV) from 10 simulations for each vessel were computed to determine reliability. Measurements with CVs less than 10% were considered reliable. Results: For normal vessels, the precision and accuracy of the integrated density technique were 0.12mm{sup 2} and 0.28mm{sup 2}, respectively. The corresponding results for manual segmentation were 0.27mm{sup 2} and 0.43mm{sup 2}. For diseased vessels, the precision and accuracy of the integrated density technique were 0.14mm{sup 2} and 0.19mm{sup 2}. Corresponding results for manual segmentation were 0.42mm{sup 2} and 0.71mm{sup 2}. Reliable CSAs were obtained for normal vessels with diameters larger than 1 mm and for diseased vessels with area as low as 1.26mm2. Conclusion: The CSA based on integrated density showed improved precision and accuracy as compared with manual segmentation in simulation. These results indicate the potential of using integrated density to quantify CSA of coronary arteries in CT angiography.

60 APPLIED LIFE SCIENCES↗

Structures of the CRISPR genome integration complex

CRISPR-Cas systems depend on the Cas1-Cas2 integrase to capture and integrate short foreign DNA fragments into the CRISPR locus, enabling adaptation to new viruses. In this paper, we present crystal structures of Cas1-Cas2 bound to both donor and target DNA in intermediate and product integration complexes, as well as a cryo–electron microscopy structure of the full CRISPR locus integration complex, including the accessory protein IHF (integration host factor). The structures show unexpectedly that indirect sequence recognition dictates integration site selection by favoring deformation of the repeat and the flanking sequences. IHF binding bends the DNA sharply, bringing an upstream recognition motif into contact with Cas1 to increase both the specificity and efficiency of integration. Lastly, these results explain how the Cas1-Cas2 CRISPR integrase recognizes a sequence-dependent DNA structure to ensure site-selective CRISPR array expansion during the initial step of bacterial adaptive immunity.

59 BASIC BIOLOGICAL SCIENCES↗

A Landing Pad System for Multicopy Gene Integration in Issatchenkia orientalis

The robust nature of the non-conventional yeast Issatchenkia orientalis allows it to grow under highly acidic conditions and therefore, has gained increasing interest in producing organic acids using a variety of carbon sources. Recently, the development of a genetic toolbox for I. orientalis, including an episomal plasmid, characterization of multiple promoters and terminators, and CRISPR-Cas9 tools, has eased the metabolic engineering efforts in I. orientalis. However, multiplex engineering is still hampered by the lack of efficient multicopy integration tools. To facilitate the construction of large, complex metabolic pathways by multiplex CRISPR-Cas9-mediated genome editing, we developed a bioinformatics pipeline to identify and prioritize genome-wide intergenic loci and characterized 47 gRNAs located in 21 intergenic regions. These loci are screened for guide RNA cutting efficiency, integration efficiency of a gene cassette, the resulting cellular fitness, and GFP expression level. We further developed a landing pad system using components from these well-characterized loci, which can aid in the integration of multiple genes using single guide RNA and multiple repair templates of the user’s choice. We have demonstrated the use of the landing pad for simultaneous integrations of 2, 3, 4, or 5 genes to the target loci with efficiencies greater than 80%. As a proof of concept, we showed how the production of 5-aminolevulinic acid can be improved by integrating five copies of genes at multiple sites in one step. We have further demonstrated the efficiency of this tool by constructing a metabolic pathway for succinic acid production by integrating five gene expression cassettes using a single guide RNA along with five different repair templates, leading to the production of 9 g/L of succinic acid in batch fermentations. This study demonstrates the effectiveness of a single gRNA-mediated CRISPR platform to build complex metabolic pathways in a non-conventional yeast. This landing pad system will be a valuable tool for the metabolic engineering of I. orientalis.

Fatma, Zia↗

PIPES (Pipeline for Integrated Projects in Energy Systems) [SWR-24-89]

The Pipeline for Integrated Projects in Energy Systems (PIPES) is a comprehensive project, data, and workflow management tool designed for integrated modeling teams. PIPES facilitates the management of data requirements, tasks, and progress tracking, serving as a higher-level integration layer that works across various data and modeling software. This tool integrates models, data, and tools to perform large-scale, integrated analysis work at scale. PIPES is designed to streamline integrated modeling projects, enhance collaboration, and ensure the quality and efficiency of data management and workflow processes. https://github.com/nrel-pipes/pipes-api https://github.com/nrel-pipes/pipes-web https://github.com/nrel-pipes/nrel-pipes

Gu, Jianli↗