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The study purpose was to report failure patterns in Masaoka-Koga stage II to IV type C thymic epithelial tumor (TET) after postoperative radiation therapy (PORT) and to evaluate the suitability of PORT target volume confined to the “tumor bed only with margin.”.
Patient-specific hemodynamic simulations have the possibility to greatly improve both the diagnosis and treatment of a variety of vascular diseases. Portability will enable wider adoption of computational fluid dynamics (CFD) applications in the biomedical research community and targeting to platforms ideally suited to different vascular regions. Here, we introduce a case study in performance portability that assesses (1) the ease of porting an MPI application optimized for one specific architecture to new platforms using variants of hybrid MPI+X programming models; (2) performance portability seen when simulating blood flow in three different vascular regions on diverse heterogeneous architectures; (3) model-based performance prediction for future architectures; and (4) performance scaling of the hybrid MPI+X programming on parallel heterogeneous systems. We report on the lessons learned in porting HARVEY, a massively parallel CFD application, from traditional multicore CPUs to diverse heterogeneous architectures ranging from NVIDIA/AMD GPUs to Intel MICs and Altera FPGAs.
Due to its high performance and throughput capabilities, GPU-accelerated computing is becoming a popular technology in scientific computing, in particular using programming models such as CUDA and OpenACC. The main advantage with OpenACC is that it enables to simply port codes in their ‘‘original’’ form to GPU systems through compiler directives, thus allowing an incremental approach. An OpenACC implementation is applied to the CFD code Nek5000 for simulation of incompressible flows, based on the spectral-element method. The work follows up previous implementations and focuses now on the P N - P N-2 method for the spatial discretization of the Navier–Stokes equations. Performance results of the ported code show a speed-up of up to 3.1 on multi-GPU for a polynomial order N > 11.
Conventional parallel-opposed radiotherapy (PORT) is the established standard technique for early-stage glottic carcinoma. However, case reports have reported the utility of intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc therapy (VMAT) with or without image guidance (image-guided radiotherapy, IGRT) in select patients. The proposed advantages of IMRT/VMAT include sparing of the carotid artery, thyroid gland, and the remaining functional larynx, although these benefits remain unclear. The following case study presents a patient with multiple vascular comorbidities treated with VMAT for early-stage glottic carcinoma. A detailed explanation of the corresponding treatment details, dose-volume histogram (DVH) analysis, and a review of the relevant literature are provided. Conventional PORT remains the standard of care for early-stage glottic carcinoma. IMRT or VMAT may be beneficial for select patients, although great care is necessary to avoid a geographical miss. Clinical data supporting the benefit of CRT are lacking. Therefore, these techniques should be used with caution and only in selected patients.
A new facility was designed around the thermal column beam port of the 1 MW Research Reactor at the University of Massachusetts Lowell. Thermal neutrons are collimated to a 1-inch diameter beam and incident on samples to induce the radiative neutron capture. New measurements of capture gamma rays are planned for Mn, Cu, Ni, Cr, and Gd samples in the next few years. The experiments will be carried out in close collaboration with the ENSDF (Evaluated Nuclear Structure Data File) evaluation group at Brookhaven National Laboratory. The gamma rays are measured using an array of high-resolution HPGe detectors. Some of the HPGe detectors use active Compton shields that were designed from scintillation detectors and improve significantly the signal-to-background in the measured gamma-ray spectra with HPGe. The experimental spectra will be validated by the GEANT4 simulations of the array and theoretical models of the emission of gamma rays from the compound nucleus. In conclusion, the new experimental results on the capture gamma ray intensities will be incorporated in future ENSDF evaluations.
We investigate linear resonant absorption by a dense ensemble of molecules confined to a sub-wavelength layer in two geometries: (i) a free-standing film in a homogeneous space and (ii) the same film placed at a controlled distance from a reflecting surface. In both cases, increasing the effective light–matter coupling (via molecular density/oscillator strength) produces a nonmonotonic response: absorption rises to an optimum and then decreases as the film becomes increasingly radiatively bright and reflective. Finite-difference time-domain simulations and analytical transfer-matrix calculations agree quantitatively and yield compact ridge conditions for the optimum. We interpret the trends using a scattering/port picture: the isolated film is a symmetric two-port system (reflection and transmission), which bounds single-sided resonant absorption to ≤50% in the ultrathin limit (reflecting transition saturation), whereas adding a mirror suppresses transmission and converts the structure into an effectively one-port absorber. In the mirror-backed geometry, interference can cancel reflection, and unity absorption is obtained at critical coupling, when radiative leakage is balanced by intrinsic molecular loss. These results clarify fundamental limits and design rules for collective absorption in dense molecular layers near dielectric or metallic boundaries.
Cloud microphysics is one of the most time-consuming components in a climate model. In this study, we port the cloud microphysics parameterization in the Community Atmosphere Model (CAM), known as Parameterization of Unified Microphysics Across Scales (PUMAS), from CPU to GPU to seek a computational speedup. The directive-based methods (OpenACC and OpenMP target offload) are determined as the best fit specifically for our development practices, which enable a single version of source code to run either on the CPU or GPU, and yield a better portability and maintainability. Their performance is first examined in a PUMAS stand-alone kernel and the directive-based methods can outperform a CPU node as long as there is enough computational burden on the GPU. A consistent behavior is observed when we run PUMAS on the GPU in a practical CAM simulation. A 3.6× speedup of the PUMAS execution time, including data movement between CPU and GPU, is achieved at a coarse horizontal resolution (8 NVIDIA V100 GPUs against 36 Intel Skylake CPU cores). This speedup further increases up to 5.4× at a high resolution (24 NVIDIA V100 GPUs against 108 Intel Skylake CPU cores), which highlights the fact that GPU favors larger problem size. This study demonstrates that using GPU in a CAM simulation can save noticeable computational costs even with a small portion of code being GPU-enabled. Therefore, we are encouraged to port more parameterizations to GPU to take advantage of its computational benefit.
Abstract This manuscript presents a detailed characterization of active control of bow shock waves via leading edge injection, including subsonic coolant ejection and the appearance of Coanda effects. The flow phenomena occurring at steady and pulsating flow injection regimes were analyzed using steady and unsteady two-dimensional Reynolds-Averaged Navier Stokes, leading to a precise evaluation of the thermal load and drag reductions. Steady supersonic injection yields the largest abatement in thermal load and aerodynamic drag, while subsonic or fluctuating ones can also provide significant improvements at reduced cooling mass flow rates. Furthermore, a Coanda effect, causing a non-symmetric flow topology, was observed and analyzed for reduced injection port size. This Coanda effect is due to the sudden expansion happening from the injection port to the main flow and it causes the flow topology at the leading edge to become non-symmetric despite the complete symmetry of the problem. This is the first time in the literature such a phenomenon is documented for a supersonic airfoil leading edge injection. Furthermore, it enables the design of novel flow control strategies for the leading edge shock topology and flow structures in supersonic flows.
Water is a strong mid-infrared absorber, which has hindered the full exploitation of label-free and non-invasive infrared (IR) spectromicroscopy techniques for the study of living biological samples. To overcome this barrier, many researchers have built sophisticated fluidic chambers or microfluidic chips wherein the depth of the liquid medium in the sample compartment is limited to 10 μm or less. We report an innovative and simple way to fabricate plastic devices with infrared transparent view-ports enabling infrared spectromicroscopy of living biological samples; therefore the device is named “IR-Live”. Advantages of this approach include lower production costs, a minimal need to access a micro-fabrication facility, and unlimited mass or waste exchange for the living samples surrounding the view-port area. We demonstrate that the low-cost IR-Live in combination with microfluidic perfusion techniques enables long term (>60 h) cell culture, which broadens the capability of IR spectromicroscopy for studying living biological samples. To illustrate this, we first applied the device to study protein and lipid polarity in migrating REF52 fibroblasts by collecting 2-dimensional spectral chemical maps at a micrometer spatial resolution. Then, we demonstrated the suitability of our approach to study dynamic cellular events by collecting a time series of spectral maps of U937 monocytes during the early stage of cell attachment to a bio-compatible surface.
With an increased dataset obtained during the Run 3 of the LHC at CERN and the even larger expected increase of the dataset by more than one order of magnitude for the HL-LHC, the ATLAS experiment is reaching the limits of the current data processing model in terms of traditional CPU resources based on x86_64 architectures and an extensive program for software upgrades towards the HL-LHC has been set up. The ARM architecture is becoming a competitive and energy efficient alternative. Some surveys indicate its increased presence in HPCs and commercial clouds, and some WLCG sites have expressed their interest. Chip makers are also developing their next generation solutions on ARM architectures, sometimes combining ARM and GPU processors in the same chip. Consequently it is important that the ATLAS software embraces the change and is able to successfully exploit this architecture. We report on the successful porting to ARM of the Athena software framework, which is used by ATLAS for both online and offline computing operations. Furthermore we report on the successful validation of simulation workflows running on ARM resources. For this we have set up an ATLAS Grid site using ARM compatible middleware and containers on Amazon Web Services (AWS) ARM resources. The ARM version of Athena is fully integrated in the regular software build system and distributed in the same way as other software releases. In addition, the workflows have been integrated into the HEPscore benchmark suite which is the planned WLCG wide replacement of the HepSpec06 benchmark used for Grid site pledges. In the overall porting process we have used resources on AWS, Google Cloud Platform (GCP) and CERN. A performance comparison of different architectures and resources will be discussed.
With the large dataset expected from 2030 onwards by the HL-LHC at CERN, the ATLAS experiment is reaching the limits of the current data processing model in terms of traditional CPU resources based on x86_64 architectures and an extensive program for software upgrades towards the HL-LHC has been set up. The ARM CPU architecture is becoming a competitive and energy efficient alternative. Accelerators like GPUs are available in any recent HPC. In the past years ATLAS has successfully ported its full data processing and simulation software framework Athena to ARM and has invested significant effort in porting parts of the reconstruction and simulation algorithms to GPUs. We report on the successful usage of the ATLAS experiment offline and online software framework Athena on ARM and GPUs through the PanDA workflow management system at various WLCG sites. Furthermore we report on performance optimizations of the builds for ARM CPUs and the GPU integration efforts. We will discuss performance comparisons of different ARM and x86_64 architectures on WLCG resources and Cloud compute providers like GCP and AWS using ATLAS productions workflows as used in the Hep-Score23 benchmark suite.
This paper describes the application of the beam emission spectroscopy (BES) to Heliotron J, having the nonsymmetrical helical-magnetic-axis configuration. The spectral and spatial profile of the beam emission has been estimated by the numerical calculation taking the collisional excitation processes between plasmas (electrons/ions) and beam atoms. Two sets of the sightlines with good spatial resolution are presented. One is the optimized viewing chords which have 20 sightlines and observe the whole plasma region with the spatial resolution {Delta}{rho} less than {+-}0.055 using the newly designed viewing port. The other is 15 sightlines from the present viewing port of Heliotron J for the preliminary measurement to discuss the feasibility of the density fluctuation measurement by BES. The beam emission has been measured by a monochromator with a CCD camera. A good consistency has been obtained between the spectral profiles of the beam emission measured by the monochromator and the beam emission spectrum deduced by the model calculation. An avalanche photodiode with an interference filter system was also used to evaluate the signal-to-noise (S/N) ratio of the beam emission in the present experimental setup. The modification of the optical system is being planned to improve the S/N ratio, which will enable us to estimate the density fluctuation in Heliotron J.
We report in this paper experimental measurements in order to validate the concept of switchable electromagnetic band gap filters based on plasma capillaries in the microwave regime. The plasma tube is embedded inside the structure to create a bistable (plasma on or off) punctual defect. We first investigate two kinds of discharge tubes: Ar-Hg and pure Ne, which we then use to experimentally achieve plasma-based reconfigurable applications, namely, a two-port coupler and a two-port demultiplexer.
A method and first results utilizing a network analyzer as a loaded cavity probe to study the resonance properties of a plasma filled electron cyclotron resonance ion source (ECRIS) plasma chamber are presented. The loaded cavity measurements have been performed using a dual port technique, in which two separate waveguides were used simultaneously. One port was used to ignite and sustain the plasma with a microwave source operating around 11 GHz and the other was used to probe the cavity properties with the network analyzer using a frequency range around 14 GHz. The first results obtained with the JYFL 14 GHz ECRIS demonstrate that the presence of plasma has significant effects on the resonance properties of the cavity. With plasma the frequency dependent behavior is strongly damped and this trend strengthens with increasing microwave power.
We consider a mirror-symmetric resonator with two ports. We show that, when excited from a single port, complete absorption can be achieved through critical coupling to degenerate resonances with opposite symmetry. Moreover, any time two resonances with opposite symmetry are degenerate in frequency and absorption is always significantly enhanced. In contrast, when two resonances with the same symmetry are nearly degenerate, there is no absorption enhancement. We numerically demonstrate these effects using a graphene monolayer on top of a photonic crystal slab, illuminated from a single side in the near-infrared.
Full function integrated, compact silicon photodiode based solid state neutral particle analyzers (ssNPA) have been developed for energetic particle (EP) relevant studies on the Experimental Advanced Superconducting Tokamak (EAST). The ssNPAs will be mostly operated in advanced current mode with a few channels to be operated in conventional pulse-counting mode, aiming to simultaneously achieve individually proved ultra-fast temporal, spatial, and spectral resolution capabilities. The design details together with considerations on EAST specific engineering realities and physics requirements are presented. The system, including a group of single detectors on two vertical ports and two 16-channel arrays on a horizontal port, can provide both active and passive charge exchange measurements. ssNPA detectors, with variable thickness of ultra thin tungsten dominated foils directly deposited on the front surface, are specially fabricated and utilized to achieve about 22 keV energy resolution for deuterium particle detection.
A simple gas cell design, constructed primarily from commercially available components, enables in situ soft X-ray transmission-absorption spectroscopy of materials in contact with gas at ambient temperature. The cell has a minimum X-ray path length of 1 mm and can hold gas pressures up to ~300 Torr, and could support higher pressures with simple modifications. The design enables cycling between vacuum and gas environments without interrupting the X-ray beam, and can be fully sealed to allow for measurements of air-sensitive samples. The cell can attach to the downstream port of any appropriate synchrotron beamline, and offers a robust and versatile method for in situ measurements of certain materials. The construction and operation of the cell are discussed, as well as sample preparation and proper spectral analysis, illustrated by examples of spectral measurements. Potential areas for improvement and modification for specialized applications are also mentioned.
Time structure of Balmer H{sub α} line intensity in Linac4 RF plasma has been analyzed by the combined simulation model of atomic transport and Collisional-Radiative models. As a preliminary result, time variation of the line intensity in the ignition phase of RF plasma is calculated and compared with the experimental results by photometry. For the comparison, spatial distribution of the local H{sub α} photon emission rate at each time is calculated from the numerical model. The contribution of the local photon emission rates to the observed line intensity via optical viewing port is also investigated by application of the mock-up of the optical viewing port and the known light source. It has been clarified from the analyses that the higher and the lower peaks of the H{sub α} line intensity observed during 1 RF cycle is mainly due to the different spatial distributions in the electron energy distribution function and the resultant local photon emission rate. These results support previous suggestion that the existence of the capacitive electric field in axial direction leads to the higher/lower peaks of the line intensity.