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At least 217 records · Page 12

New Modeling Approaches to Study DNA Damage by the Direct and Indirect Effects of Ionizing Radiation

DNA is damaged both by the direct and indirect effects of radiation. In the direct effect, the DNA itself is ionized, whereas the indirect effect involves the radiolysis of the water molecules surrounding the DNA and the subsequent reaction of the DNA with radical products. While this problem has been studied for many years, many unknowns still exist. To study this problem, we have developed the computer code RITRACKS [1], which simulates the radiation track structure for heavy ions and electrons, calculating all energy deposition events and the coordinates of all species produced by the water radiolysis. In this work, we plan to simulate DNA damage by using the crystal structure of a nucleosome and calculations performed by RITRACKS. The energy deposition events are used to calculate the dose deposited in nanovolumes [2] and therefore can be used to simulate the direct effect of the radiation. Using the positions of the radiolytic species with a radiation chemistry code [3] it will be possible to simulate DNA damage by indirect effect. The simulation results can be compared with results from previous calculations such as the frequencies of simple and complex strand breaks [4] and with newer experimental data using surrogate markers of DNA double ]strand breaks such as . ]H2AX foci [5].

Plante, Ianik↗

Vertex-finding and reconstruction of contained two-track neutrino events in the MicroBooNE detector

In this work, we describe algorithms developed to isolate and accurately reconstruct two-track events that are contained within the MicroBooNE detector. This method is optimized to reconstruct two tracks of lengths longer than 5cm. This code has applications to searches for neutrino oscillations and measurements of cross sections using quasi-elastic-like charged current events. The algorithms we discuss will be applicable to all detectors running in Fermilab's Short Baseline Neutrino program (SBN), and to any future liquid argon time projection chamber (LArTPC) experiment with beam energies ~ 1 GeV. The algorithms are publicly available on a GITHUB repository. This reconstruction offers a complementary and independent alternative to the Pandora reconstruction package currently in use in LArTPC experiments, and provides similar reconstruction performance for two-track events.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Quasi-optical beam tracing module development for millimeter-wave high-wavenumber collective scattering on the NSTX-U and EAST tokamaks

A Python3-based beam tracing code utilizing Quasi-Optics has been developed to track both incident and receiving beams in high-k collective millimeter wave scattering systems within magnetic fusion plasmas. In contrast to existing ray tracing codes that solely consider refraction, this beam tracing code incorporates diffraction phenomena, providing a more comprehensive calculation. Here, this enhanced capability allows for a more accurate calculation of the scattering volume and spatial resolution in high-k collective scattering systems, crucial for evaluating system performance and facilitating data analysis. Unlike Geometrical Optics, Quasi-Optics employs the complex eikonal method, representing a Gaussian beam as a collection of coupled rays to accurately preserve diffraction characteristics. The developed code is intended for application in NSTX-Upgrade and EAST high-k beam tracing analyses, targeting frequencies of 693 GHz and 270 GHz, respectively. The high-k system's primary objective is the observation of electron-scale instabilities. Employing a symplectic integrator, the code ensures numerical accuracy, assessed through the conservation of the Hamiltonian. With its precision and efficiency, the code facilitates rapid inter-shot analyses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Simulations of particle interactions in a high-current RFQ

High-intensity beams of composite ions are susceptible to particle interactions that do not affect single ions, such as stripping of electrons and charge exchange. Beam dynamics simulation techniques used in accelerator design do not often include these particle interactions, and so the transmission of the real beam can be significantly different from the design simulations. We have modified the IMPACT-T code to include particle interactions as part of the beam dynamics simulations, including space-charge effects and beam losses. We have carried out validation simulations of interactions in a molecular hydrogen ion beam through an existing high-intensity deuteron RFQ design, as beam commissioning is often carried out using molecular hydrogen beams, to avoid deuteron-deuteron interactions in the accelerator leading to neutron activation. The new code framework successfully models the interactions within the beam, tracks the different source and product ions through the accelerator, and calculates the collective effects such as space charge from all particles together. Finally, we also discuss other simulation codes that could be modified to include similar interaction effects, and possible applications to other types of accelerators.

47 OTHER INSTRUMENTATION↗

Model Energy Codes End-Use Opportunity Analysis

Model energy codes (ASHRAE Standard 90.1 and IECC) has significantly impacted programs and policies aimed at improving energy efficiency both in United States and across the globe. Standard 90.1, first published in 1975 (originally referred to as Standard 90) provides minimum energy efficiency guidelines for designing, constructing, operating, and maintaining new construction and renovated buildings. It is updated continuously, with new editions published every 3 years. Pacific Northwest National Laboratory (PNNL) conducts simulated energy and cost savings analysis of model energy codes to determine their expected impact and to track progress toward net-zero goals and efficiency targets. Additionally, the simulation outputs are examined to assess how energy is used across primary systems within prominent U.S. commercial building types to understand how energy is used in each building type at the end-use level and to identify areas for improvements in future code cycles. This end-use opportunity analysis of model energy codes provides ASHRAE technical committees and other interested parties a better understanding of how the Standard affects various building systems and end uses, specifically, those in the Standard that most prominently influence energy efficiency. Additionally, findings provide industry stakeholders guidance in identifying building types and end-uses with the most potential for energy efficiency improvements through energy codes and those that may require beyond code measures to meet energy use reduction targets. This paper summarizes features and functionalities of a webtool created by PNNL to explore and visualize the End-Use opportunity analysis.

ASHRAE 90.1, Energy Codes, Tableau↗

Validation of a synthetic fast ion loss detector model for Wendelstein 7-X

Abstract We present the first validated synthetic diagnostic for fast ion loss detectors (FILDs) in the Wendelstein 7-X (W7-X) stellarator. This model has been developed on, and validated against experimental data from, a FILD provided by the National Institute for Fusion Science (NIFS-FILD), with potential future applicability to the existing Faraday Cup FILD (FC-FILD) on W7-X as well as the scintillating FILD (S-FILD) currently under development. A workflow combining Monte Carlo codes BEAMS3D and ASCOT5 is used to track fast ions produced by neutral beam injection from the moment of ionization until they are thermalized or lost from the last closed flux surface, and from there to a virtual plane which serves as a projection of the entrance aperture to the FILD. Simulations in ASCOT5 are analyzed via a geometric method to determine the probability of transmission through the FILD aperture and onto the detector as a function of normalized momentum, pitch angle, gyrophase, and position at the virtual plane. This probability is then applied to the simulated ions arriving from the plasma, producing a simulated signal from a computationally tractable number of simulated fast ions. Simulated signals are presented for two W7-X experiments with neutral beam injection and quantitatively compared with experimental measurements from the NIFS-FILD diagnostic. An estimate of the frequency of charge-exchange with neutral particles in the edge is performed, and it is found that this process may have a significant impact on the measured signals.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Optimizing injection for the storage ring proton-EDM experiment

The proposed proton electric dipole moment (pEDM) experiment at Brookhaven National Laboratory (BNL), to be built inside the alternating gradient synchrotron (AGS) tunnel, aims to measure the proton’s electric dipole moment with a sensitivity of 10 −29 𝑒 cm. This paper presents the design of the injection line from the AGS booster to the pEDM storage ring, utilizing portions of the existing booster-to-AGS (BtA) transfer line. Building on the symmetric-hybrid lattice design [, Comprehensive symmetric-hybrid ring design for a proton-EDM experiment at below 10 −29 𝑒 cm, Phys. Rev. D 105, 032001 (2022)], our study emphasizes rigorous optics matching, detailed particle and spin tracking, and systematic error mitigation essential for achieving a target sensitivity of 10 −29 𝑒 cm. This design preserves the proton’s vertical spin orientation within ±20 mrad, a critical requirement for the pEDM measurement. Particle and spin tracking simulations using the ray-tracing code Zgoubi [F. Méot, Zgoubi users’ guide, Technical Report, Brookhaven National Laboratory (BNL), Relativistic Heavy Ion Collider (RHIC), Upton, NY, 2012] validate the design’s performance, demonstrating its feasibility for this precision experiment. The simulation results demonstrate that both clockwise (CW) and counterclockwise (CCW) injection lines meet the stringent beam envelope and polarization requirements.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

LaPT (Lab Process Tracker) [SWR-26-048]

LaPT (Lab Process Tracker) is a QR/barcode scanning infrastructure for tracking samples and processes. It is a tracking application for lab operations with a graphical user interface. Track processes and sample scans using QR code input, with logs saved to CSV files.

Daxini, Rajiv [National Laboratory of the Rockies ↗

Processing MCNP Elemental Edit Outputs

The Los Alamos National Laboratory's (LANL) Monte Carlo N-Particle® (MCNP®) transport code version 6 has the capability for tracking particles on unstructured mesh (UM) geometry models. The MCNP UM feature was originally designed for the UM models created by the Abaqus/CAE software product. The MCNP version 6.2.0 and later recognizes the UM models read from Abaqus INP files or MCNPUM files converted from Abaqus INP files. Other finite element analysis software packages may generate UM models and then convert these models into Abaqus INP formats.

97 MATHEMATICS AND COMPUTING↗

Generating MCNP Input Files for Unstructured Mesh Geometries

Los Alamos National Laboratory's (LANL) Monte Carlo N-Particle (MCNP) transport code version 6 has the capability for tracking particles on unstructured mesh (UM) geometry models. The MCNP UM feature has been developed for performing calculations of complex geometry models. This capability tracks particles on hybrid geometries where finite element meshes are embedded into constructive solid geometry (CSG) cells. The MCNP UM feature was originally designed to read UM models created by Abaqus/CAE software suite. MCNP versions 6.2.0 and later can process UM models read from Abaqus input les or MCNPUM les converted from Abaqus input les. Sandia National Laboratory's Cubit Toolkit and other finite element analysis software packages may generate UM models and then convert these models into Abaqus input formats.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

GSC configuration management plan

The tools and methods used for the configuration management of the artifacts (including software and documentation) associated with the Guidance and Control Software (GCS) project are described. The GCS project is part of a software error studies research program. Three implementations of GCS are being produced in order to study the fundamental characteristics of the software failure process. The Code Management System (CMS) is used to track and retrieve versions of the documentation and software. Application of the CMS for this project is described and the numbering scheme is delineated for the versions of the project artifacts.

Withers, B. Edward↗

Discrete X-Ray Source Populations and Star-Formation History in Nearby Galaxies

This program aims in understanding the connection between the discrete X-ray source populations observed in nearby galaxies and the history of star-formation in these galaxies. The ultimate goal is to use this knowledge in order to constrain X-ray binary evolution channels. For this reason although the program is primarily observational it has a significant modeling component. During the first year of this study we focused on the definition of a pilot sample of galaxies with well know star-formation histories. A small part of this sample has already been observed and we performed initial analysis of the data. However, the majority of the objects in our sample either have not been observed at all, or the detection limit of the existing observations is not low enough to probe the bulk of their young X-ray binary populations. For this reason we successfully proposed for additional Chandra observations of three targets in Cycle-5. These observations are currently being performed. The analysis of the (limited) archival data for this sample indicated that the X-ray luminosity functions (XLF) of the discrete sources in these galaxies may not have the same shape as is widely suggested. However, any solid conclusions are hampered by the small number of detected sources. For this reason during the second year of this study, we will try to extend the sample in order to include more objects in each evolutionary stage. In addition we are completing the analysis of the Chandra monitoring observations of the Antennae galaxies. The results from this work, apart from important clues on the nature of the most luminous sources (Ultra-luminous X-ray sources; ULXs) provide evidence that source spectral and/or temporal variability does not significantly affect the shape of their X-ray luminosity functions. This is particularly important for comparisons between the XLFs of different galaxies and comparisons with predictions from theoretical models. Results from this work have been presented in several conferences. Refereed journal papers presenting these conclusions are currently in preparation. An important part of this study is the Chandra survey of the Small Magellanic Cloud, our second nearest star- forming galaxy. So far we have been awarded 5 Chandra observations of the central youngest part of the galaxy. These observations will help to study the very faint end of the young X-ray binary populations which is not possible to probe in more distant objects. Results from this study have been presented in several conferences and two papers are in preparation. In addition during year-2 we are planning of undertaking the task of identifying optical counterparts to the X-ray sources, which will help us to isolate interlopers (sources not associated with the SMC) and classify the X-ray binaries which are found to be associated with the SMC. In the theoretical front, the Star-Track X-ray binary population synthesis code which will be used for the modeling of the X-ray binary populations (led by co-I V. Kalogera and C. Belczynski), is complete. A first test using the XLF of the star-forming galaxy NGC-1569 showed remarkable agreement between the observed and the modeled XLF. These results are presented in an ApJ. Letters paper (Belczynski et al, 2004, 601, 147). During year-2 of this study we are planning of performing a parameter study in order to investigate which parameters are most important for the shape of the XLF. In addition we will perform comparisons with observations of other galaxies from our sample as they become available.

Zezas, Andreas↗

Using Docker Containers to Extend Reproducibility Architecture for the NASA Earth Exchange (NEX)

NASA Earth Exchange (NEX) is a data, supercomputing and knowledge collaboratory that houses NASA satellite, climate and ancillary data where a focused community can come together to address large-scale challenges in Earth sciences. As NEX has been growing into a petabyte-size platform for analysis, experiments and data production, it has been increasingly important to enable users to easily retrace their steps, identify what datasets were produced by which process chains, and give them ability to readily reproduce their results. This can be a tedious and difficult task even for a small project, but is almost impossible on large processing pipelines. We have developed an initial reproducibility and knowledge capture solution for the NEX, however, if users want to move the code to another system, whether it is their home institution cluster, laptop or the cloud, they have to find, build and install all the required dependencies that would run their code. This can be a very tedious and tricky process and is a big impediment to moving code to data and reproducibility outside the original system. The NEX team has tried to assist users who wanted to move their code into OpenNEX on Amazon cloud by creating custom virtual machines with all the software and dependencies installed, but this, while solving some of the issues, creates a new bottleneck that requires the NEX team to be involved with any new request, updates to virtual machines and general maintenance support. In this presentation, we will describe a solution that integrates NEX and Docker to bridge the gap in code-to-data migration. The core of the solution is saemi-automatic conversion of science codes, tools and services that are already tracked and described in the NEX provenance system, to Docker - an open-source Linux container software. Docker is available on most computer platforms, easy to install and capable of seamlessly creating and/or executing any application packaged in the appropriate format. We believe this is an important step towards seamless process deployment in heterogeneous environments that will enhance community access to NASA data and tools in a scalable way, promote software reuse, and improve reproducibility of scientific results.

earth exchange↗

Novel features and GPU performance analysis for EM particle transport in the Celeritas code

Celeritas is a new computational transport code designed for high-performance simulation of high-energy physics detectors. This work describes some of its current capabilities and the design choices that enable the rapid development of efficient on-device physics. The abstractions that underpin the code design facilitate low-level performance tweaks that require no changes to the higher-level physics code. We evaluate a set of independent changes that together yield an almost 40% speedup over the original GPU code for a net performance increase of 220× for a single GPU over a single CPU running 8.4M tracks on a small demonstration physics app.

Johnson, Seth R.↗

Performance Analysis of PIConGPU: Particle-in-Cell on GPUs using NVIDIA’s NSight Systems and NSight Compute

PIConGPU, Particle In Cell on GPUs, is an open source simulations framework for plasma and laser-plasma physics used to develop advanced particle accelerators for radiation therapy of cancer, high energy physics and photon science. While PIConGPU has been optimized for at least 5 years to run well on NVIDIA GPU-based clusters, there has been limited exploration by the development team of potential scalability bottlenecks using recently updated and new tools including NVIDIA’s NVProf tool and the brand-new NVIDIA NSight Suite (Systems and Compute) tools. PIConGPU is a highly optimized application that runs production jobs at scale on a system Oak Ridge Leadership Facility’s (OLCF) Summit supercomputer (using the full machine at 4600 nodes; at 98% of GPU utilization on all ~28000 NVIDIA Volta GPUs). PIConGPU has been selected as one of the the eight applications for OLCF’s coveted Center for Accelerated Application Readiness (CAAR) program aimed at the facility’s Frontier supercomputer (OLCF’s first exascale system to launch in 2021), to partner with our vendors (primary vendors: AMD and Cray/HPE) ensuring that Frontier will be able to perform large-scale science when it opens to users in 2022. To this effect, performance engineers on the PIConGPU team wanted to dive deep into the application to understand at the finest granularity, which portions of the code could be further optimized to exploit the hardware on Summit at it’s maximum potential and also to elucidate which key kernels should be tracked and optimized for the CAAR effort to port this code to Frontier. Any bottlenecks that are observed via performance profiling on Summit are likely to also impact scalability on the Frontier-dev system and the Frontier Early Access (EA) system. Additionally, the engineers wanted to take a closer look at the newest NVIDIA profiling tools which allows us to identify the most useful features on these tools and will provide an opportunity to compare it to new AMD and Cray’s performance analysis tool releases and provide feedback to our vendor partners on what features are most important and mission critical for CAAR efforts. The primary goal of this report is to focus on the evaluation of PIConGPU’s most time-intensive kernels using NVProf and NSight Suite. Three kernels, Current Deposition (also known as Compute Current), Particle Push (Move and Mark), and Shift Particles are known to be some of the most time-consuming kernels in PIConGPU. The Current xi Deposition kernel and Particle Push kernel both set up the particle attributes for running any physics simulation with PIConGPU, so it is crucial to improve the performance of these two kernels. In this report, we measure single GPU metrics for the three kernels, offer high level takeaways from the conducted analysis, and compare the profiling data from NSight Compute to that of NVProf. This analysis was performed using a grid size of 240 x 272 x 224, and 10 time steps with the Mid-November Figure of Merit (FOM) run setup. The Traveling Wave Electron Acceleration (TWEAC) science case used in this run is a representative science case for PIConGPU. This execution can also be used for baseline analysis on AMD MI50/ MI60 systems. As of the time of writing, the PIConGPU application has limited use for features of NSight Systems, so this report will mainly focus on insights garnered from NSight Compute. For this analysis, we run the “full” metric set available in NSight Compute version 2020.1.2 and use NSight Systems version 2020.3.1 to generate the application timeline.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Two-dimensional particle displacement tracking in particle imaging velocimetry

A new particle imaging velocimetry data acquisition and analysis system, which is an order of magnitude faster than any previously proposed system, has been constructed and tested. The new particle displacement tracking (PDT) system is an all electronic technique employing a video camera and a large memory buffer frame-grabber board. Using a simple encoding scheme, a time sequence of single exposure images is time-coded into a single image and then processed to track particle displacements and determine two-dimensional velocity vectors. Use of the PDT technique in a counterrotating vortex flow produced over 1100 velocity vectors in 110 s when processed on an 80386 PC.

Wernet, Mark P.↗

Designing and Developing Web-Based Administrative Tools for Program Management

The task assigned for this internship was to develop a new tool for tracking projects, their subsystems, the leads, backups, and other employees assigned to them, as well as all the relevant information related to the employee (WBS (time charge) codes, time distribution, certifications, and assignments). Currently, this data is tracked manually using a number of different spreadsheets and other tools simultaneously by a number of different people; some of these documents are then merged into one large document. This often leads to inconsistencies and loss in data due to human error. By simplifying the process of tracking this data and aggregating it into a single tool, it is possible to significantly decrease the potential for human error and time spent collecting and checking this information. II. Objective The main objective of this internship is to develop a web-based tool using Ruby on Rails to serve as a method of easily tracking projects, subsystems, and points of contact, along with employees, their assignments, time distribution, certifications, and contact information. Additionally, this tool must be capable of generating a number of different reports based on the data collected. It was important that this tool deliver all of this information using a readable and intuitive interface.

Material↗

Convolutional coding at 50 Mbps for the Shuttle Ku-band return link

Error correcting coding is required for 50 Mbps data link from the Shuttle Orbiter through the Tracking and Data Relay Satellite System (TDRSS) to the ground because of severe power limitations. Convolutional coding has been chosen because the decoding algorithms (sequential and Viterbi) provide significant coding gains at the required bit error probability of one in 10 to the sixth power and can be implemented at 50 Mbps with moderate hardware. While a 50 Mbps sequential decoder has been built, the highest data rate achieved for a Viterbi decoder is 10 Mbps. Thus, five multiplexed 10 Mbps Viterbi decoders must be used to provide a 50 Mbps data rate. This paper discusses the tradeoffs which were considered when selecting the multiplexed Viterbi decoder approach for this application.

Batson, B. H.↗