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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

SU-F-T-306: Validation of Mobius 3D and FX for Elekta Linear Accelerators

Purpose: Log file based IMRT and VMAT QA is a system that analyzes treatment log files and uses delivery parameters to compute the dose to the patient/phantom. This system was previously commissioned for Varian machines, the purpose of this work is to describe the process for commissioning Mobius for use with Elekta machines. Methods: Twelve IMRT and VMAT plans (6×) were planned and delivered and dose was measured using MapCheck, the results were compared to that computed by Mobius. For 10x and 18x, plans were generated, copied to a phantom and delivered, the dose was measured using a single ion chamber. The difference in measured dose to computed dose (Mobius) was used to adjust the dynamic leaf gap (DLG) in Mobius to achieve optimal agreement between measurements, Mobius and treatment plans. Results: For the measured dose comparison, the average 3%/3mm gamma 97.1% of pixels passed criteria using MapCheck where Mobius computed 96.9% of voxels passing. For 10×, a DLG of −5.5 was determined to achieve optimal results for TPS and measured ion chamber data with an average 0.1% difference and −1.7% respectively. For 18×, a DLG of −3 was determined to achieve optimal results from the TPS and measured data with an average of −0.7% and −1.4% difference on average from a set of IMRT and VMAT plans. The 6x data needed no DLG correction to arrive at agreement with the TPS and the MapCheck measured data. Conclusion: We have validated with measurements for IMRT and VMAT cases the use of Mobius FX with Elekta treatment machines for IMRT and VMAT QA. For 6×, no adjustments to the DLG were required to obtain good results utilizing Mobius whereas for 10× and 18×, the DLG had to be adjusted to obtain optimum agreement with measured data and our TPS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-308: Mobius FX Evaluation and Comparison Against a Commercial 4D Detector Array for VMAT Plan QA

Purpose: To evaluate the use of MobiusFX as a pre-treatment verification IMRT QA tool and compare it with a commercial 4D detector array for VMAT plan QA. Methods: 15 VMAT plan QA of different treatment sites were delivered and measured by traditional means with the 4D detector array ArcCheck (Sun Nuclear corporation) and at the same time measurement in linac treatment logs (Varian Dynalogs files) were analyzed from the same delivery with MobiusFX software (Mobius Medical Systems). VMAT plan QAs created in Eclipse treatment planning system (Varian) in a TrueBeam linac machine (Varian) were delivered and analyzed with the gamma analysis routine from SNPA software (Sun Nuclear corporation). Results: Comparable results in terms of the gamma analysis with 99.06% average gamma passing with 3%,3mm passing rate is observed in the comparison among MobiusFX, ArcCheck measurements, and the Treatment Planning System dose calculated. When going to a stricter criterion (1%,1mm) larger discrepancies are observed in different regions of the measurements with an average gamma of 66.24% between MobiusFX and ArcCheck. Conclusion: This work indicates the potential for using MobiusFX as a routine pre-treatment patient specific IMRT method for quality assurance purposes and its advantages as a phantom-less method which reduce the time for IMRT QA measurement. MobiusFX is capable of produce similar results of those by traditional methods used for patient specific pre-treatment verification VMAT QA. Even the gamma results comparing to the TPS are similar the analysis of both methods show that the errors being identified by each method are found in different regions. Traditional methods like ArcCheck are sensitive to setup errors and dose difference errors coming from the linac output. On the other hand linac log files analysis record different errors in the VMAT QA associated with the MLCs and gantry motion that by traditional methods cannot be detected.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-457: A Filmless Method for Measurement of Couch Translation Per Gantry Rotation and Couch Speed for Tomotherapy Using ArcCheck

Purpose: To develop a filmless methodology based on an ArcCheck for QA measurement of the couch translation per gantry rotation and couch speed of a Tomotherapy unit. Methods: Two test plans recommended by TG148 were chosen for this study. A helical plan with 1 cm field size opened the leaves for 180 degrees at the 2nd, 7th and 12th of total 13 rotations and was used to verify if the couch travelled the expected distance per gantry rotation. The other test plan was a static plan with the gantry at 0°, 1cm field width and constant couch movement speed of 0.5mm/s. It was used for couch speed measurement. The ArcCheck was isocentrically set up and recorded movie files which took a snapshot exposure every 50ms. Due to the spiral pattern of diodes distribution, when one of the diodes of the ArcCheck located at the beam center, the dose profile as measured by the row of diodes which surrounded the center diode should have a symmetrical pattern. We divided the profile into left half A and right half B. Then a shape parameter was defined as S=Σ|(A−B)|/Σ(A+B). By searching the local minimum of S parameter, the beam center at different time could be located. The machine trajectory log data were also collected and analyzed for comparison. Results: The mean value of measured couch translation and couch speed by ArcCheck had less than 0.05% deviation from the planned values. For couch speed measurement, our result showed a mean value of 0.5002 with an uncertainty ±0.0031, which agreed very well with both the plan setting of 0.5 mm/s and the machine log data of 0.5005 mm/s. Conclusion: Couch translation measured using ArcCheck is accurate and comparable to the film-based measurement. This filmless method also provides a convenient and independent way for measuring couch speed.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2024

Global producer responsibility for plastic pollution

Brand names can be used to hold plastic companies accountable for their items found polluting the environment. We used data from a 5-year (2018–2022) worldwide (84 countries) program to identify brands found on plastic items in the environment through 1576 audit events. We found that 50% of items were unbranded, calling for mandated producer reporting. The top five brands globally were The Coca-Cola Company (11%), PepsiCo (5%), Nestlé (3%), Danone (3%), and Altria (2%), accounting for 24% of the total branded count, and 56 companies accounted for more than 50%. There was a clear and strong log-log linear relationship production (%) = pollution (%) between companies’ annual production of plastic and their branded plastic pollution, with food and beverage companies being disproportionately large polluters. Phasing out single-use and short-lived plastic products by the largest polluters would greatly reduce global plastic pollution.

Science & Technology - Other Topics↗
DOE OSTI2017

Conductance distribution near the Anderson transition

Using a modification of the Shapiro approach, we introduce the two-parameter family of conductance distributions W(g), defined by simple differential equations, which are in the one-to-one correspondence with conductance distributions for quasi-one-dimensional systems of size L{sup d–1} × L{sub z}, characterizing by parameters L/ξ and L{sub z}/L (ξ is the correlation length, d is the dimension of space). This family contains the Gaussian and log-normal distributions, typical for the metallic and localized phases. For a certain choice of parameters, we reproduce the results for the cumulants of conductance in the space dimension d = 2 + ϵ obtained in the framework of the σ-model approach. The universal property of distributions is existence of two asymptotic regimes, log-normal for small g and exponential for large g. In the metallic phase they refer to remote tails, in the critical region they determine practically all distribution, in the localized phase the former asymptotics forces out the latter. A singularity at g = 1, discovered in numerical experiments, is admissible in the framework of their calculational scheme, but related with a deficient definition of conductance. Apart of this singularity, the critical distribution for d = 3 is well described by the present theory. One-parameter scaling for the whole distribution takes place under condition, that two independent parameters characterizing this distribution are functions of the ratio L/ξ.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

High-frequency underwater plasma discharge application in antibacterial activity

Plasma discharge is a novel disinfection and effectual inactivation approach to treat microorganisms in aqueous systems. Inactivation of Gram-negative Escherichia coli (E. coli) by generating high-frequency, high-voltage, oxygen (O{sub 2}) injected and hydrogen peroxide (H{sub 2}O{sub 2}) added discharge in water was achieved. The effect of H{sub 2}O{sub 2} dose and oxygen injection rate on electrical characteristics of discharge and E. coli disinfection has been reported. Microbial log reduction dependent on H{sub 2}O{sub 2} addition with O{sub 2} injection was observed. The time variation of the inactivation efficiency quantified by the log reduction of the initial E. coli population on the basis of optical density measurement was reported. The analysis of emission spectrum recorded after discharge occurrence illustrated the formation of oxidant species (OH{sup •}, H, and O). Interestingly, the results demonstrated that O{sub 2} injected and H{sub 2}O{sub 2} added, underwater plasma discharge had fabulous impact on the E. coli sterilization. The oxygen injection notably reduced the voltage needed for generating breakdown in flowing water and escalated the power of discharge pulses. No impact of hydrogen peroxide addition on breakdown voltage was observed. A significant role of oxidant species in bacterial inactivation also has been identified. Furthermore the E. coli survivability in plasma treated water with oxygen injection and hydrogen peroxide addition drastically reduced to zero. The time course study also showed that the retardant effect on E. coli colony multiplication in plasma treated water was favorable, observed after long time. High-frequency underwater plasma discharge based biological applications is technically relevant and would act as baseline data for the development of novel antibacterial processing strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Evolution of Optical Diffraction Patterns on Disordered Woodpile Photonic Structures

Using three-dimensional direct laser writing, ordered and disordered photonic woodpile structures have been produced. An ideal woodpile is formed by layers of parallel “logs” turned through 90° with respect to logs of the previous layer. The disorder was specified by a random deviation in the angle with respect to their parallel arrangement in each layer of the woodpile. The quality of samples was tested by scanning electron microscopy. The optical diffraction patterns were studied experimentally on microsamples with different degrees of disorder and structure periods. With an increase in the degree of the disorder, the diffraction patterns changed qualitatively with the preservation of the zero diffraction order and formation of a speckle field pattern by higher diffraction orders.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Laplacian Smoothing Stochastic Gradient Markov Chain Monte Carlo

As an important Markov chain Monte Carlo (MCMC) method, the stochastic gradient Langevin dynamics (SGLD) algorithm has achieved great success in Bayesian learning and posterior sampling. Furthermore, SGLD typically suffers from a slow convergence rate due to its large variance caused by the stochastic gradient. In order to alleviate these drawbacks, we leverage the recently developed Laplacian smoothing technique and propose a Laplacian smoothing stochastic gradient Langevin dynamics (LS-SGLD) algorithm. We prove that for sampling from both log-concave and non-log-concave densities, LS-SGLD achieves strictly smaller discretization error in 2-Wasserstein distance, although its mixing rate can be slightly slower. Experiments on both synthetic and real datasets verify our theoretical results and demonstrate the superior performance of LS-SGLD on different machine learning tasks including posterior sampling, Bayesian logistic regression, and training Bayesian convolutional neural networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Pulse-shape discrimination against low-energy Ar-39 beta decays in liquid argon with 4.5 tonne-years of DEAP-3600 data

The DEAP-3600 detector searches for the scintillation signal from dark matter particles scattering on a 3.3 tonne liquid argon target. The largest background comes from 39 Ar beta decays and is suppressed using pulse-shape discrimination (PSD). We use two types of PSD estimator: the prompt-fraction, which considers the fraction of the scintillation signal in a narrow and a wide time window around the event peak, and the log-likelihood-ratio, which compares the observed photon arrival times to a signal and a background model. We furthermore use two algorithms to determine the number of photons detected at a given time: (1) simply dividing the charge of each PMT pulse by the mean single-photoelectron charge, and (2) a likelihood analysis that considers the probability to detect a certain number of photons at a given time, based on a model for the scintillation pulse shape and for afterpulsing in the light detectors. The prompt-fraction performs approximately as well as the log-likelihood-ratio PSD algorithm if the photon detection times are not biased by detector effects. We explain this result using a model for the information carried by scintillation photons as a function of the time when they are detected.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Access Patterns and Performance Behaviors of Multi-layer Supercomputer I/O Subsystems under Production Load

Scientific computing workloads at HPC facilities have been shifting from traditional numerical simulations to AI/ML applications for training and inference while processing and producing ever-increasing amounts of scientific data. To address the growing need for increased storage capacity, lower access latency, and higher bandwidth, emerging technologies such as non-volatile memory are integrated into supercomputer I/O subsystems. With these emerging trends, we need a better understanding of the multilayer supercomputer I/O systems and ways to use these subsystems efficiently. In this work, we study the I/O access patterns and performance characteristics of two representative supercomputer I/O subsystems. Through an extensive analysis of year-long I/O logs on each system, we report new observations in I/O reads and writes, unbalanced use of storage system layers, and new trends in user behaviors at the HPC I/O middleware stack.

Bez, JL↗
DOE OSTI2025

DEDUPKV: A Space-Efficient and High-Performance Key-Value Store via Fine-Grained Deduplication

Log-Structured Merge Tree (LSM-tree) based key-value stores excel in write-intensive environments but suffer from data duplication, consuming up to 49% of storage space in LSM-tree-based key-value store deployments. Traditional solutions like compression and coarse-grained file system-level deduplication introduce overhead or have limited effectiveness. In this study, we propose DedupKV, a fine-grained deduplication framework tailored for LSM-tree, maximizing data reduction efficiency while minimizing write stalls and read overheads. DedupKV features three key innovations: (1) FLUSH-integrated inline deduplication, which removes duplicates during memory-to-storage writes; (2) WAL file-based offline deduplication, repurposing write-ahead logs to avoid double writes; and (3) elastic execution, dynamically balancing inline and offline deduplication based on memory pressure and workload intensity. Additionally, dynamic granularity management reduces deduplication metadata overhead. We implemented these four ideas in RocksDB for the first time and conducted experiments in a Linux environment. Our evaluation shows that WAL file-based offline deduplication and DedupKV outperform BlobDB by 33% and 23%, respectively, in write-heavy workloads, while reducing write amplification by 1.2 ×, 2 ×, and 1.6 × for real KV datasets.

Jamil, Safdar [Sogang University]↗
DOE OSTI2020

Analysis of Electric Vehicle Charging Behavior Patterns with Function Principal Component Analysis Approach

This manuscript focused on analyzing electric vehicles’ (EV) charging behavior patterns with a functional data analysis (FDA) approach, with the goal of providing theoretical support to the EV infrastructure planning and regulation, as well as the power grid load management. 5-year real-world charging log data from a total of 455 charging stations in Kansas City, Missouri, was used. The focuses were placed on analyzing the daily usage occupancy variability, daily energy consumption variability, and station-level usage variability. Compared with the traditional discrete-based analysis models, the proposed FDA modeling approach had unique advantages in preserving the smooth function behavior of the data, bringing more flexibility in the modeling process with little required assumptions or background knowledge on independent variables, as well as the capability of handling time series data with different lengths or sizes. In addition to the patterns revealed in the EV charging station’s occupancy and energy consumption, the differences between EV driver’s charging time and parking time were analyzed and called for the needs for parking regulation and enforcement. The different usage patterns observed at charging stations located on different land-use types were also analyzed.

Engineering↗
DOE OSTI2022

Assessment of Spoilage Microbiota of Rainbow Trout (Oncorhynchus mykiss) during Storage by 16S rDNA Sequencing

Due to the high contents of protein and fat in rainbow trout, it is highly susceptible to spoilage, which limits the storage and transportation processes. Exploring the spoilage microbial community during rainbow trout storage is essential to develop an effective preservation method. Here, the changes in the total bacterial colony and total volatile base nitrogen (TVB-N) during the storage of rainbow trout were investigated. Storage at 0 °C can effectively slow down the spoilage process with bacterial counts and TVB-N contents decreased from 8.7 log CFU/g and 18.7 mg/100 g obtained at 4 °C to 5.6 log CFU/g and 14.5 mg/100 g, respectively. 16S rDNA high-throughput sequencing results showed that the diversity of microbial genera decreased during storage. Acinetobacter, Pseudomonas, and Shewanells gradually became the dominant spoilage genera with contents of 59.9%, 18.6%, and 1.7%, respectively, in the late stage of storage. The spoilage abilities of bacteria belonging to the Pseudomonas and Shewanells genera were analyzed. Shewanella sp. S5-52 showed the highest level of TVB-N content (100.6 mg/100 g) in sterile fish juice, indicating that it had a strong spoilage ability. This study confirmed the dominant spoilage bacterial genera and evaluated the spoilage abilities of isolated strains during the storage of rainbow trout, which laid the foundation for further investigation of the spoilage mechanism of rainbow trout and other aquatic products.

Du, Guangqing↗
DOE OSTI2018

Anno v1

The Anno log annotation system provides tools for creating and querying annotations to supercomputing log data.

Greiner, AnnetteM↗
DOE OSTI2020

Logic in Memory Emulator

Logic in Memory Emulator (LiME) is a hardware/software tool specially designed for memory system evaluation and experiment. Emerging memories display a wide range of bandwidths, latencies, and capacities, making it challenging for the computer architect to navigate the design space of potential memory configurations, and for the application developer to assess performance implications of using such memories. With the LiME framework, architectural ideas can be prototyped in great detail yet with sufficient performance to support realistic evaluation on long running applications. LiME consists of two fundamental components: 1) the hardware and OS infrastructure for the emulator, and 2) a suite of benchmark applications to assist in characterizing the performance of current and future computer architectures. Some of the applications have been collected from other open source projects. Uses: Logging, replay and analysis of an application's memory behavior Evaluate impact of emerging memory technology on application performance. Emulate complex memory interactions in whole applications orders of magnitude faster than software simulation. Emulate acceleration hardware co-located with the memory subsystem. Features: Capture and log external memory accesses to a separate off-chip memory device without affecting application execution. Memory traces include the address, length, timestamp, and optionally the data for each transaction. Captured trace data can be saved to an SD card for off-line analysis. Configure a wide range of memory latencies in sub-nanosecond increments that encompass highbandwidth and storage class memories. Specify regions of interest (ROI) in applications to reduce the amount of trace data captured for analysis. Currently supports execution on Xilinx Zynq SoC which integrates an ARM processor with FPGA logic on a single device. Applications can be run under Linux or in bare metal mode on the ARM cores.

Jain, AbhishekK↗
DOE OSTI2020

PAM module for OAuth 2.0 Device flow

This is a PAM module that lets you log in via SSH to servers using OpenID Connect credentials, instead of SSH Keys or a username and password combination. It uses the OAuth2 Device Flow, which means that during the login process, you will click a link and log in to your OpenID Connect Provider, which will then authenticate you for the SSH session. This module will then check if you're in the right group(s) or have a specified username, and allow or deny access.

Surkont, Jarosław↗
DOE OSTI2021

yuwangcn/C4_dynamic_model

A dynamic systems model of C4 photosynthesis was developed based on the previous NADP-ME metabolic model for maize (Wang et al., 2014 ab). The NADP-ME metabolic model is an ordinary differential equation model including all individual steps in C4 photosynthetic carbon metabolism. Here, the model is extended to include posttranslational regulation and temperature response of enzyme activities, dynamic stomata conductance, and leaf energy balance. This model is written in Matlab (R2019a) Steady-state and dynamic gas exchange data for maize (B73), sugarcane (CP88-1762) and sorghum (Tx430) were measured in a greenhouse in Urbana, IL from July 25, 2019 through August 8, 2019. Data include: CO2 response curves Light response curves Photosynthetic induction curves measured in the transition from darkness to high light (1800 μmol m-2 s-1), data logged every 1 min. Photosynthetic induction in the transition from darkness to high light (1800 μmol m-2 s-1) to determine the kinetics of rubisco activation in these C4 crops (τ_Rubisco), data logged every 10 s. Gas exchange under fluctuating light. After dark adaptation, the leaves undergo three light change steps, light intensity was set as 1800 µmol m-2 s-1, 200 µmol m-2 s-1 and 1800 µmol m-2 s-1 for each 1800 s step.

Wang, Yu↗
DOE OSTI2025

OLCF Test Harness

Acceptance and regression testing of a High Performance Computing (HPC) system requires an automated and reproducible framework and tool for running and logging results. Manually running tests across a system is labor intensive and prone to reproducibility errors. The OLCF Test Harness (OTH) provides a framework in which to document required tests for a HPC system. The OTH then provides tools to execute and log results of these tests in an automated fashion.

Dietz, Dan [Oak Ridge National Laboratory (ORNL), ↗