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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

SU-G-TeP2-15: Feasibility Study of Fiber-Optic Cerenkov Radiation Sensors for in Vivo Measurement: Dosimetric Characterization and Clinical Application in Proton Beams

Purpose: To evaluate the possibility of a fiber-optic Cerenkov radiation sensor (FCRS) for in vivo dose verification in proton therapy. Methods: The Cerenkov radiation due to the proton beam was measured using a homemade phantom, consisting of a plastic optical fiber (POF, PGSCD1001-13-E, Toray, Tokyo, Japan) connected to each channel of a multianode photomultiplier tube (MAPMT:H7546, Hamamatsu Photonics, Shizuoka, Japan). Data were acquired using a multi-anode photomultiplier tube with the NI-DAQ system (National Instruments Texas, USA). The real-time monitoring graphic user interface was programmed using Labview. The FCRS was analyzed for its dosimetrics characteristic in proton beam. To determine the accuracy of the FCRS in proton dose measurements, we compared the ionization chamber dose measurements using a water phantom. We investigated the feasibility of the FCRS for the measurement of dose distributions near the superficial region for proton plans with a varying separation between the target volume and the surface of 3 patients using a humanoid phantom. Results: The dose-response has good linearity. Dose-rate and energy dependence were found to be within 1%. Depth-dose distributions in non-modulated proton beams obtained with the FCRS was in good agreement with the depth-dose measurements from the ionization chamber. To evaluate the dosimetric accuracy of the FCRS, the difference of isocenter dose between the delivery dose calculated by the treatment planning system and that measured by the FCRS was within 3%. With in vivo dosimetry using the humanoid phantom, the calculated surface doses overestimated measurements by 4%–8% using FCRS. Conclusion: In previous study, our results indicate that the performance of the array-type FCRS was comparable to that of the currently used a multi-layer ion chamber system. In this study, we also believe that the fiber-optic Cerenkov radiation sensor has considerable potential for use with in vivo patient proton dosimetry.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2016

MO-DE-BRA-02: SIMAC: A Simulation Tool for Teaching Linear Accelerator Physics

Purpose: The first goal of this work is to develop software that can simulate the physics of linear accelerators (linac). The second goal is to show that this simulation tool is effective in teaching linac physics to medical physicists and linac service engineers. Methods: Linacs were modeled using analytical expressions that can correctly describe the physical response of a linac to parameter changes in real time. These expressions were programmed with a graphical user interface in order to produce an environment similar to that of linac service mode. The software, “SIMAC”, has been used as a learning aid in a professional development course 3 times (2014 – 2016) as well as in a physics graduate program. Exercises were developed to supplement the didactic components of the courses consisting of activites designed to reinforce the concepts of beam loading; the effect of steering coil currents on beam symmetry; and the relationship between beam energy and flatness. Results: SIMAC was used to teach 35 professionals (medical physicists; regulators; service engineers; 1 week course) as well as 20 graduate students (1 month project). In the student evaluations, 85% of the students rated the effectiveness of SIMAC as very good or outstanding, and 70% rated the software as the most effective part of the courses. Exercise results were collected showing that 100% of the students were able to use the software correctly. In exercises involving gross changes to linac operating points (i.e. energy changes) the majority of students were able to correctly perform these beam adjustments. Conclusion: Software simulation(SIMAC), can be used to effectively teach linac physics. In short courses, students were able to correctly make gross parameter adjustments that typically require much longer training times using conventional training methods.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MO-FG-CAMPUS-TeP1-03: Pre-Treatment Surface Imaging Based Collision Detection

Purpose: Modern radiotherapy increasingly employs large immobilization devices, gantry attachments, and couch rotations for treatments. All of which raise the risk of collisions between the patient and the gantry / couch. Collision detection is often achieved by manually checking each couch position in the treatment room and sometimes results in extraneous imaging if collisions are detected after image based setup has begun. In the interest of improving efficiency and avoiding extra imaging, we explore the use of a surface imaging based collision detection model. Methods: Surfaces acquired from AlignRT (VisionRT, London, UK) were transferred in wavefront format to a custom Matlab (Mathworks, Natick, MA) software package (CCHECK). Computed tomography (CT) scans acquired at the same time were sent to CCHECK in DICOM format. In CCHECK, binary maps of the surfaces were created and overlaid on the CT images based on the fixed relationship of the AlignRT and CT coordinate systems. Isocenters were added through a graphical user interface (GUI). CCHECK then compares the inputted surfaces to a model of the linear accelerator (linac) to check for collisions at defined gantry and couch positions. Note, CCHECK may be used with or without a CT. Results: The nominal surface image field of view is 650 mm × 900 mm, with variance based on patient position and size. The accuracy of collision detections is primarily based on the linac model and the surface mapping process. The current linac model and mapping process yield detection accuracies on the order of 5 mm, assuming no change in patient posture between surface acquisition and treatment. Conclusions: CCHECK provides a non-ionizing method to check for collisions without the patient in the treatment room. Collision detection accuracy may be improved with more robust linac modeling. Additional gantry attachments (e.g. conical collimators) can be easily added to the model.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TU-D-201-06: HDR Plan Prechecks Using Eclipse Scripting API

Purpose: Automate brachytherapy treatment plan quality check using Eclipse v13.6 scripting API based on pre-configured rules to minimize human error and maximize efficiency. Methods: The HDR Precheck system is developed based on a rules-driven approach using Eclipse scripting API. This system checks for critical plan parameters like channel length, first source position, source step size and channel mapping. The planned treatment time is verified independently based on analytical methods. For interstitial or SAVI APBI treatment plans, a Patterson-Parker system calculation is performed to verify the planned treatment time. For endobronchial treatments, an analytical formula from TG-59 is used. Acceptable tolerances were defined based on clinical experiences in our department. The system was designed to show PASS/FAIL status levels. Additional information, if necessary, is indicated appropriately in a separate comments field in the user interface. Results: The HDR Precheck system has been developed and tested to verify the treatment plan parameters that are routinely checked by the clinical physicist. The report also serves as a reminder or checklist for the planner to perform any additional critical checks such as applicator digitization or scenarios where the channel mapping was intentionally changed. It is expected to reduce the current manual plan check time from 15 minutes to <1 minute. Conclusion: Automating brachytherapy plan prechecks significantly reduces treatment plan precheck time and reduces human errors. When fully developed, this system will be able to perform TG-43 based second check of the treatment planning system’s dose calculation using random points in the target and critical structures. A histogram will be generated along with tabulated mean and standard deviation values for each structure. A knowledge database will also be developed for Brachyvision plans which will then be used for knowledge-based plan quality checks to further reduce treatment planning errors and increase confidence in the planned treatment.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2016

A tracking system to calculate patient skin dose in real-time during neurointerventional procedures using a biplane x-ray imaging system

Purpose: Neurovascular interventional procedures using biplane fluoroscopic imaging systems can lead to increased risk of radiation-induced skin injuries. The authors developed a biplane dose tracking system (Biplane-DTS) to calculate the cumulative skin dose distribution from the frontal and lateral x-ray tubes and display it in real-time as a color-coded map on a 3D graphic of the patient for immediate feedback to the physician. The agreement of the calculated values with the dose measured on phantoms was evaluated. Methods: The Biplane-DTS consists of multiple components including 3D graphic models of the imaging system and patient, an interactive graphical user interface, a data acquisition module to collect geometry and exposure parameters, the computer graphics processing unit, and functions for determining which parts of the patient graphic skin surface are within the beam and for calculating dose. The dose is calculated to individual points on the patient graphic using premeasured calibration files of entrance skin dose per mAs including backscatter; corrections are applied for field area, distance from the focal spot and patient table and pad attenuation when appropriate. The agreement of the calculated patient skin dose and its spatial distribution with measured values was evaluated in 2D and 3D for simulated procedure conditions using a PMMA block phantom and an SK-150 head phantom, respectively. Dose values calculated by the Biplane-DTS were compared to the measurements made on the phantom surface with radiochromic film and a calibrated ionization chamber, which was also used to calibrate the DTS. The agreement with measurements was specifically evaluated with variation in kVp, gantry angle, and field size. Results: The dose tracking system that was developed is able to acquire data from the two x-ray gantries on a biplane imaging system and calculate the skin dose for each exposure pulse to those vertices of a patient graphic that are determined to be in the beam. The calculations are done in real-time with a typical graphic update time of 30 ms and an average vertex separation of 3 mm. With appropriate corrections applied, the Biplane-DTS was able to determine the entrance dose within 6% and the spatial distribution of the dose within 4% compared to the measurements with the ionization chamber and film for the SK150 head phantom. The cumulative dose for overlapping fields from both gantries showed similar agreement. Conclusions: The Biplane-DTS can provide a good estimate of the peak skin dose and cumulative skin dose distribution during biplane neurointerventional procedures. Real-time display of this information should help the physician manage patient dose to reduce the risk of radiation-induced skin injuries.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Technical Note: SCUDA: A software platform for cumulative dose assessment

Purpose: Accurate tracking of anatomical changes and computation of actually delivered dose to the patient are critical for successful adaptive radiation therapy (ART). Additionally, efficient data management and fast processing are practically important for the adoption in clinic as ART involves a large amount of image and treatment data. The purpose of this study was to develop an accurate and efficient Software platform for CUmulative Dose Assessment (SCUDA) that can be seamlessly integrated into the clinical workflow. Methods: SCUDA consists of deformable image registration (DIR), segmentation, dose computation modules, and a graphical user interface. It is connected to our image PACS and radiotherapy informatics databases from which it automatically queries/retrieves patient images, radiotherapy plan, beam data, and daily treatment information, thus providing an efficient and unified workflow. For accurate registration of the planning CT and daily CBCTs, the authors iteratively correct CBCT intensities by matching local intensity histograms during the DIR process. Contours of the target tumor and critical structures are then propagated from the planning CT to daily CBCTs using the computed deformations. The actual delivered daily dose is computed using the registered CT and patient setup information by a superposition/convolution algorithm, and accumulated using the computed deformation fields. Both DIR and dose computation modules are accelerated by a graphics processing unit. Results: The cumulative dose computation process has been validated on 30 head and neck (HN) cancer cases, showing 3.5 ± 5.0 Gy (mean±STD) absolute mean dose differences between the planned and the actually delivered doses in the parotid glands. On average, DIR, dose computation, and segmentation take 20 s/fraction and 17 min for a 35-fraction treatment including additional computation for dose accumulation. Conclusions: The authors developed a unified software platform that provides accurate and efficient monitoring of anatomical changes and computation of actually delivered dose to the patient, thus realizing an efficient cumulative dose computation workflow. Evaluation on HN cases demonstrated the utility of our platform for monitoring the treatment quality and detecting significant dosimetric variations that are keys to successful ART.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗
DOE OSTI2015

Software package for modeling spin–orbit motion in storage rings

A software package providing a graphical user interface for computer experiments on the motion of charged particle beams in accelerators, as well as analysis of obtained data, is presented. The software package was tested in the framework of the international project on electric dipole moment measurement JEDI (Jülich Electric Dipole moment Investigations). The specific features of particle spin motion imply the requirement to use a cyclic accelerator (storage ring) consisting of electrostatic elements, which makes it possible to preserve horizontal polarization for a long time. Computer experiments study the dynamics of 10{sup 6}–10{sup 9} particles in a beam during 10{sup 9} turns in an accelerator (about 10{sup 12}–10{sup 15} integration steps for the equations of motion). For designing an optimal accelerator structure, a large number of computer experiments on polarized beam dynamics are required. The numerical core of the package is COSY Infinity, a program for modeling spin–orbit dynamics.

43 PARTICLE ACCELERATORS↗
DOE OSTI2016

Fluctuating Hydrodynamics Methods for Dynamic Coarse-Grained Implicit-Solvent Simulations in LAMMPS

We present a software package integrated with the molecular dynamics software LAMMPS for fluctuating hydrodynamics simulations of fluid-structure interactions subject to thermal fluctuations. The package is motivated to provide dynamic thermostats to extend implicit-solvent coarse-grained (IS-CG) models by incorporating kinetic contributions from the solvent to facilitate their use in a wider range of applications. To capture the thermal and hydrodynamic contributions of the solvent to dynamics, we introduce momentum conserving thermostats and computational methods based on fluctuating hydrodynamics and the stochastic Eulerian Lagrangian method (SELM). SELM couples the coarse-grained microstructure degrees of freedom to continuum stochastic fields to capture both the relaxation of hydrodynamic modes and thermal fluctuations. Features of the SELM software include (i) numerical time-step integrators for SELM fluctuating hydrodynamics in inertial and quasi-steady regimes, (ii) Lees--Edwards-style methods for imposing shear, (iii) a Java-based graphical user interface (GUI) for setting up models and simulations, (iv) standardized XML formats for parametrization and data output, and (v) standardized formats VTK for continuum fields and microstructures. The SELM software package facilitates for pre-established models in LAMMPS easy adoption of the SELM fluctuating hydrodynamics thermostats. We offer here an overview of the SELM software package, computational methods, and applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

GrammarViz 3.0: Interactive Discovery of Variable-Length Time Series Patterns

The problems of recurrent and anomalous pattern discovery in time series, e.g., motifs and discords, respectively, have received a lot of attention from researchers in the past decade. However, since the pattern search space is usually intractable, most existing detection algorithms require that the patterns have discriminative characteristics and have its length known in advance and provided as input, which is an unreasonable requirement for many real-world problems. In addition, patterns of similar structure, but of different lengths may co-exist in a time series. In order to address these issues, we have developed algorithms for variable-length time series pattern discovery that are based on symbolic discretization and grammar inference—two techniques whose combination enables the structured reduction of the search space and discovery of the candidate patterns in linear time. In this work, we present GrammarViz 3.0—a software package that provides implementations of proposed algorithms and graphical user interface for interactive variable-length time series pattern discovery. The current version of the software provides an alternative grammar inference algorithm that improves the time series motif discovery workflow, and introduces an experimental procedure for automated discretization parameter selection that builds upon the minimum cardinality maximum cover principle and aids the time series recurrent and anomalous pattern discovery.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

PETSc DMNetwork: A Library for Scalable Network PDE-Based Multiphysics Simulations

We present DMNetwork, a high-level package included in the PETSc library for the simulation of multiphysics phenomena over large-scale networked systems. The library aims at applications that have networked structures such as those in electrical, gas, and water distribution systems. DMNetwork provides data and topology management, parallelization for multiphysics systems over a network, and hierarchical and composable solvers to exploit the problem structure. DMNetwork eases the simulation development cycle by providing the necessary infrastructure through simple abstractions to define and query the network components. This article presents the design of DMNetwork, illustrates its user interface, and demonstrates its ability to solve multiphysics systems, such as an electric circuit, a network of power grid and water subnetworks, and transient hydraulic systems over large networks with more than 2 billion variables on extreme-scale computers using up to 30,000 processors.

extreme-scale computing↗
DOE OSTI2013

Development of a Neural Network Simulator for Studying the Constitutive Behavior of Structural Composite Materials

This paper introduces a recent development and application of a noncommercial artificial neural network (ANN) simulator with graphical user interface (GUI) to assist in rapid data modeling and analysis in the engineering diffraction field. The real-time network training/simulation monitoring tool has been customized for the study of constitutive behavior of engineering materials, and it has improved data mining and forecasting capabilities of neural networks. This software has been used to train and simulate the finite element modeling (FEM) data for a fiber composite system, both forward and inverse. The forward neural network simulation precisely reduplicates FEM results several orders of magnitude faster than the slow original FEM. The inverse simulation is more challenging; yet, material parameters can be meaningfully determined with the aid of parameter sensitivity information. The simulator GUI also reveals that output node size for materials parameter and input normalization method for strain data are critical train conditions in inverse network. The successful use of ANN modeling and simulator GUI has been validated through engineering neutron diffraction experimental data by determining constitutive laws of the real fiber composite materials via a mathematically rigorous and physically meaningful parameter search process, once the networks are successfully trained from the FEM database.

Na, Hyuntae↗
DOE OSTI2012

n-dimensional Statistical Inverse Graphical Hydraulic Test Simulator

nSIGHTS (n-dimensional Statistical Inverse Graphical Hydraulic Test Simulator) is a comprehensive well test analysis software package. It provides a user-interface, a well test analysis model and many tools to analyze both field and simulated data. The well test analysis model simulates a single-phase, one-dimensional, radial/non-radial flow regime, with a borehole at the center of the modeled flow system. nSIGHTS solves the radially symmetric n-dimensional forward flow problem using a solver based on a graph-theoretic approach. The results of the forward simulation are pressure, and flow rate, given all the input parameters. The parameter estimation portion of nSIGHTS uses a perturbation-based approach to interpret the best-fit well and reservoir parameters, given an observed dataset of pressure and flow rate.

Kuhlman, KristopherL↗
DOE OSTI2013

QuickNXS

Data reduction software for the Oak Ridge National Laboratory Spallation Neutron Source's Magnetism Reflectometer beam line 4A, used to extract reflectivity, off-specular and GISANS scattering from raw data in NeXus file format. The package consists of a Python library for the extraction and a Qt4 based graphical user interface to work with the data.

Glavic, ArturGregor↗
DOE OSTI2013

Metadata staging tools

Django application providing a user-interface for building a file and metadata management system. Operates in conjunction with https://github.com/usgin/metadata-server.

Source record↗
DOE OSTI2013

Metadata management staging system

Django application providing a user-interface for building a file and metadata management system. An evolution of our Node.js and CouchDb metadata management system. This one focuses on server functionality and uses a well-documented, rational and REST-ful API for data access.

Source record↗
DOE OSTI2016

Sirepo for Synchrotron Radiation Workshop

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jinja, which is a secure and widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is the Synchrotron Radiation Workshop (SRW). SRW computes synchrotron radiation from relativistic electrons in arbitrary magnetic fields and propagates the radiation wavefronts through optical beamlines. SRW is open source and is primarily supported by Dr. Oleg Chubar of NSLS-II at Brookhaven National Laboratory.

Nagler, Robert↗
DOE OSTI2016

Sirepo - Warp

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure and widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.

Nagler, Robert↗