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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

3013/9975 Surveillance Program Interim Summary Report

The K-Area Materials Storage (KAMS) Documented Safety Analysis (DSA) requires a surveillance program to monitor the safety performance of 3013 containers and 9975 shipping packages stored in KAMS. The SRS surveillance program [Reference 1] outlines activities for field surveillance and laboratory tests that demonstrate the packages meet the functional performance requirements described in the DSA. The SRS program also supports the complexwide Integrated Surveillance Program (ISP) [Reference 2] for 3013 containers. The purpose of this report is to provide a summary of the SRS portion of the surveillance program activities through fiscal year 2010 (FY10) and formally communicate the interpretation of these results by the Surveillance Program Authority (SPA). Surveillance for the initial 3013 container random sampling of the Innocuous bin and the Pressure bin has been completed and there has been no indication of corrosion or significant pressurization. The maximum pressure observed was less than 50 psig, which is well below the design pressure of 699 psig for the 3013 container [Reference 3]. The data collected during surveillance of these bins has been evaluated by the Materials Identification and Surveillance (MIS) Working Group and no additional surveillance is necessary for these bins at least through FY13. A decision will be made whether additional surveillance of these bins is needed during future years of storage and as additional containers are generated. Based on the data collected to date, the SPA concludes that 3013 containers in these bins can continue to be safely stored in KAMS. This year, 13 destructive examinations (DE) were performed on random samples from the Pressure & Corrosion bin. To date, DE has been completed for approximately 30% of the random samples from the Pressure & Corrosion bin. In addition, DE has been performed on 6 engineering judgment (EJ) containers, for a total of 17 to date. This includes one container that exceeded the 3013 Standard moisture limit which was opened at LANL. The container pieces and an oxide sample were sent to SRNL for examination in FY11. No significant pressurization has been observed for the Pressure & Corrosion bin containers. Relatively minor corrosion has been observed on some convenience containers and the inside of two inner containers. While the limited extent of corrosion does not jeopardize the integrity of the outer 3013 containers, it does highlight the importance of continuing to perform DE and the Shelf Life program to assure that the corrosion rate is not accelerating or changing to a different corrosion mechanism (e.g., stress corrosion cracking). Statistical sampling is currently scheduled to be completed in FY17, but there is a proposed reduction of the number of DE's per year for FY11 and beyond which may delay the completion date. Since 3013 containers are stored inside 9975 containers, surveillances of 9975 containers are performed in conjunction with 3013 container surveillances. Results of 9975 container nondestructive examinations (NDEs) and DEs indicate that the containers will provide adequate protection of the 3013 containers in K-Area storage for at least 15 years [Reference 4].

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

What regulates decomposition in agroecosystems? Insights from reading the tea leaves

Litter decomposition is a critical Earth process, recycling nutrients and setting a portion of plant tissue on a path toward soil organic matter. Despite this importance, we still lack a good understanding of local factors that regulate decomposition, especially in agroecosystems where management plays an outsized role. Using a narrow range of climate and soils, we buried 1,308 pre-manufactured “litter bags” of differing residue quality (i.e., green and rooibos tea leaves) in 109 plots across several management practices to (1) explore the local controls on decomposition in agroecosystems and (2) test the robustness of the Tea Bag Index (TBI). We found that management practices intended to increase soil ecosystem services, that is, soil health, altered the decomposition of both teas. For example, adding nitrogen fertilizer and implementing perennial cropping decreased the extent of green tea decomposition (carbon-to-nitrogen ratio, or C:N = 12.8). No-tillage increased, but perennial cropping decreased, the rate of rooibos tea decomposition (C:N = 50.1). Cropped prairie accelerated green tea decomposition and increased the extent of red tea decomposition. A random forest regression model showed that soil temperature was the strongest predictor of green tea decomposition, but a soil health score also played a significant role in predicting the mass remaining. Soil texture and nutrient availability best predicted rooibos tea decomposition. Finer textured soils seemed to decelerate rooibos decomposition but increased the extent of decomposition. Furthermore, we demonstrated that the TBI metrics correlated somewhat well with empirically derived decomposition constants and were similarly sensitive to the effects of management. Still, the green tea stabilization factor had a substantial prediction bias. Our study increased our basic understanding of what regulates decomposition in agroecosystems. It also showed that the TBI can be a scientifically rigorous citizen science approach to monitoring changes in soil health.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Vertical Axis Wind Turbine (VAWT) with Thermoplastic Composite Blades

Rising concerns about global climate change, planet pollution and increasing use of energy have accelerated wider utilization of renewable energy sources. A recent trend in energy system development is decentralization of power generation systems. The opportunity for individuals or organizations to generate electricity locally decreases losses and part of the electricity price caused by the long-distance power transmission. Vertical axis wind turbines (VAWTs) cannot compete with traditional horizontal axis wind turbines (HAWTs) on the basis of aerodynamic performance or maximum power output generated for a given footprint. However, their ability to perform at a wide range of wind speeds, indifference to wind direction, simplicity of fabrication, transportability and maintainability make them ideal candidates for decentralized installations in urban and residential areas. The project team including Steelhead Composites (SHC), Colorado State University (CSU), National Renewable Energy Laboratory (NREL) and Arkema Inc. designed and fabricated a VAWT rotor assembly with thermoplastic composite blades using novel infusion and fabrication techniques. This full-scale VAWT rotor assembly was designed for a rated power output of 0.5-1 kW, as estimated through analytical computational fluid dynamics (CFD) methods. Those CFD simulations were combined with structural finite element analysis (FEA) to optimize the shape and composite layup of the wind blades. Much of the emphasis of this program was to characterize the recyclable thermoplastic material and composite structural design, in order to take full advantage of the material properties of such composites. Additionally, this project examined the potential of thermoplastic resin systems to transform the way VAWT rotor assemblies are joined both in the factory in in the field, by utilizing thermally welded joints to minimize field failure. The infused composite blades manufactured during this program are an excellent example of these benefits made possible by the Arkema thermoplastic resin system. This prototype blade manufacturing also provided the groundwork to inform decisions for larger scale manufacturing techniques applicable to a commercialization strategy. There is specific commercial interest for small scale VAWT’s that are competitively priced, perform to expectations, and have environmentally conscious end-of-life characteristics. Economic analysis was also conducted to compare designs and material usage, providing an estimated levelized cost of energy (LCOE) for the VAWT. The next steps for commercialization would include testing of the rotor assembly to verify predicted performance, specification of the balance of plant components (generator, inverter, etc.), and identification of a manufacturing partner with capability to scale-up production. This program has showed the potential for a commercially viable product through detailed analysis, material characterization and prototype fabrication.

17 WIND ENERGY↗
DOE OSTI2016

SU-F-T-19: The Consistency Dosimetric Analysis of the Accelerated Breast Brachytherapy

Purpose: To assess the best approach in accept a treatment plan for APBI Savi patients. Should we run a treatment verification test prior to delivering it to the patient? Should we check each CT scan in regards to the initial one in dosimetrical terms? Do we need deformable registration and adaptive planning for each fraction? These are the questions we want to answer running a dosimetric analysis of the dose variances for APBI treatments who receive 10 fractions and no re-planning has been done being considered unnecessary with today’s means of assessment. Methods: A retrospective analysis of 30 patients treated with SAVI applicators were considered for this study. The CT scans taken before each treatment were imported in the treatment planning system and registered with the initial CT scan. The images were fused together with respective to the applicator, using landmark registration. Dosimetric evaluations were performed. Dose received by skin, ribs and PTV on CT images with respect to the initial treatment plan were recorded including maximum, average and minimum dose Results: All the structures displayed changes in volume over the 10 fractions of treatment. The cavities reduction in volume was considerable with a maximum reduction of over 10%. The PTV-eval is covered better due to this fact while the critical organs manifest an increase in the total and maximum dose delivered. Ribs and skin surface that are required by B39 protocol to be monitored can acquire maximum doses of 20% to 30% respectively. Conclusion: A dosimetric evaluation prior to the initial treatment and prior to each of the 10 fractions is proven to be necessary. Deformable registration and adaptive planning have to be studied more and eventually implemented for every patient who received more than one fraction of any type of brachytherapy treatment. Immobilization ad localization methods must be improved and studied further.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

SU-E-T-204: Improving Multiple Isocenter Coincidence: Elekta Beam Modulator with HexaPOD Six Degrees Couchtop

Purpose: With evolution from frame-based to image-guided SRS/SRT technique, the coincidence of multiple isocenters must be within a tight tolerance: MV, kV, table mechanical, and, in this case, HexaPOD 6° patient positioning system. Reported here is a method for improving the effectiveness of an isocenter alignment procedure which ultimately led to isocenter coincidence on an Elekta Beam Modulator LINAC equipped with 4 mm MLC leaves and a fixed secondary jaw to within a radius of 1mm. Methods: Utilizing a self-leveling laser, the Elekta ball (BB) bearing phantom (8mm steel ball), the Modus QA Isocenter Cube software, and a colleague-provided isocenter alignment method, the kV, table mechanical, and HexaPOD isocenters were localized to the MV isocenter. Isocenter coincidence was tested using the Isocenter Cube from Modus QA, brought to kV isocenter using CBCT and the HexaPOD system. MV images were taken at various gantry, collimator, and couch angles and then analyzed with the aforementioned software to determine coincidence of the 5mm steel ball at cube center with MV isocenter. To improve overall coincidence, two errors were addressed iteratively: (1) LINAC mechanical and radiation isocenter coincidence allowing each isocenter volume to have similar variations during gantry and collimator rotation and (2) collimator rotational walkout which reduced the size of both mechanical and radiation isocenters. Beam steering was performed to bring MV isocenter closer to mechanical and collimator walkout was adjusted by physically shifting the MLC bank. Initial procedures were repeated to align all isocenters and perform regular checks for consistency. Results: Post-initial alignment revealed a maximum diameter of 1.8mm for MV isocenter and maximum isocenter alignment error of up to 1.22mm radius which improved to roughly 1.0mm MV isocenter diameter and <0.71mm radius alignment error with a consistency within 0.25mm. Conclusion: With the methods described, all isocenters were brought into alignment within a radius of 1mm.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2014

TH-C-17A-07: Visualizing and Quantifying Radiation Therapy in Real-Time Using a Novel Beam Imaging Technique

Purpose: Radiation therapy uses invisible high energy X-rays to treat an invisible tumor. Proper positioning of the treatment beam relative to the patient's anatomy during dose delivery is critically important to the success of treatment. We develop and characterize a novel radiation therapy beam visualization technique for real-time monitoring of patient treatment. Methods: Custom made flexible scintillator sheets were fabricated from gadolinium oxysulfide (GOS) particles that had been doped with terbium within a silicone elastomer matrix. Sheets of several thicknesses ranging from 0.3 to 1mm were prepared and tested. Sheets were exposed to megavoltage X-ray and electron beams from a Varian linac and the resulting optical signal was collected by multiple CMOS cameras placed in the treatment room. Real-time images were collected for different beam energies and dose rates. Signal intensity and SNR were calculated by processing the acquired images. Results: All signals were detectable in the presence of full room lighting and at an integration time of 45ms. Average signal intensity and SNR increased with both sheet thickness and dose rate and decreased with beam energy and incident light. For a given sheet thickness and beam energy the correlation between dose rate and signal intensity was highly linear. Increased sheet thickness or dose rate results in a linear increase in the detected signal. All results are consistent with analytical approximations. Conclusion: The technique offers a means of accurately visualizing a radiation therapy beam shape and fluence in real time. The effects of salient parameters have been characterized and will enable further optimization of the technique as it is implemented into the clinical workflow. The project described was supported by the National Center for Advancing Translational Sciences of the National Institutes of Health through UL1 TR001085.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-586: Pre-Treatment QA of InCise2 MLC Plans On a Cyberknife-M6 Using the Delta4 System in SBRT

Purpose: Performing pre-treatment quality assurance (QA) with the Delta4 system (ScandiDos Inc., Madison, WI) is well established for linac-based radiotherapy. This is not true when using a Cyberknife (Accuray Inc., Sunnyvale, CA) where, typically film-based QA is applied. The goal of this work was to test the feasibility to use the Delta4 system for pre-treatment QA for stereotactic body radiation therapy (SBRT) using a Cyberknife-M6 equipped with the InCise2 multileaf collimator (MLC). Methods: In order to perform measurements without accelerator pulse signal, the Tomotherapy option within the Delta4 software was used. Absolute calibration of the Delta4 phantom was performed using a 10×10 cm{sup 2} field shaped by the InCise2 MLC of the Cyberknife-M6. Five fiducials were attached to the Delta4 phantom in order to be able to track the phantom before and during measurements. For eight SBRT treatment plans (two liver, two prostate, one lung, three bone metastases) additional verification plans were recalculated on the Delta4 phantom using MultiPlan. Dicom data was exported from MultiPlan and was adapted in order to be compatible with the Delta4 software. The measured and calculated dose distributions were compared using the gamma analysis of the Delta4 system. Results: All eight SBRT plans were successfully measured with the aid of the Delta4 system. In the mean, 98.0±1.9%, 95.8±4.1% and 88.40±11.4% of measured dose points passed the gamma analysis using a global dose deviation criterion of 3% (100% corresponds to the dose maximum) and a distance-to-agreement criterion of 3 mm, 2 mm and 1 mm, respectively, and a threshold of 20%. Conclusion: Pre-treatment QA of SBRT plans using the Delta4 system on a Cyberknife-M6 is feasible. Measured dose distributions of SBRT plans showed clinically acceptable agreement with the corresponding calculated dose distributions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

Demons deformable registration of CT and cone-beam CT using an iterative intensity matching approach

Purpose: A method of intensity-based deformable registration of CT and cone-beam CT (CBCT) images is described, in which intensity correction occurs simultaneously within the iterative registration process. The method preserves the speed and simplicity of the popular Demons algorithm while providing robustness and accuracy in the presence of large mismatch between CT and CBCT voxel values (''intensity''). Methods: A variant of the Demons algorithm was developed in which an estimate of the relationship between CT and CBCT intensity values for specific materials in the image is computed at each iteration based on the set of currently overlapping voxels. This tissue-specific intensity correction is then used to estimate the registration output for that iteration and the process is repeated. The robustness of the method was tested in CBCT images of a cadaveric head exhibiting a broad range of simulated intensity variations associated with x-ray scatter, object truncation, and/or errors in the reconstruction algorithm. The accuracy of CT-CBCT registration was also measured in six real cases, exhibiting deformations ranging from simple to complex during surgery or radiotherapy guided by a CBCT-capable C-arm or linear accelerator, respectively. Results: The iterative intensity matching approach was robust against all levels of intensity variation examined, including spatially varying errors in voxel value of a factor of 2 or more, as can be encountered in cases of high x-ray scatter. Registration accuracy without intensity matching degraded severely with increasing magnitude of intensity error and introduced image distortion. A single histogram match performed prior to registration alleviated some of these effects but was also prone to image distortion and was quantifiably less robust and accurate than the iterative approach. Within the six case registration accuracy study, iterative intensity matching Demons reduced mean TRE to (2.5{+-}2.8) mm compared to (3.5{+-}3.0) mm with rigid registration. Conclusions: A method was developed to iteratively correct CT-CBCT intensity disparity during Demons registration, enabling fast, intensity-based registration in CBCT-guided procedures such as surgery and radiotherapy, in which CBCT voxel values may be inaccurate. Accurate CT-CBCT registration in turn facilitates registration of multimodality preoperative image and planning data to intraoperative CBCT by way of the preoperative CT, thereby linking the intraoperative frame of reference to a wealth of preoperative information that could improve interventional guidance.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

SU-E-T-100: Designing a QA Tool for Enhance Dynamic Wedges Based On Dynalog Files

Purpose: A robust quality assurance (QA) program for computer controlled enhanced dynamic wedge (EDW) has been designed and tested. Calculations to perform such QA test is based upon the EDW dynamic log files generated during dose delivery. Methods: Varian record and verify system generates dynamic log (dynalog) files during dynamic dose delivery. The system generated dynalog files contain information such as date and time of treatment, energy, monitor units, wedge orientation, and type of treatment. It also contains the expected calculated segmented treatment tables (STT) and the actual delivered STT for the treatment delivery as a verification record. These files can be used to assess the integrity and precision of the treatment plan delivery. The plans were delivered with a 6 MV beam from a Varian linear accelerator. For available EDW angles (10°, 15°, 20°, 25°, 30°, 45°, and 60°) Varian STT values were used to manually calculate monitor units for each segment. It can also be used to calculate the EDW factors. Independent verification of fractional MUs per segment was performed against those generated from dynalog files. The EDW factors used to calculate MUs in TPS were dosimetrically verified in solid water phantom with semiflex chamber on central axis. Results: EDW factors were generated from the STT provided by Varian and verified against practical measurements. The measurements were in agreement of the order of 1 % to the calculated EDW data. Variation between the MUs per segment obtained from dynalog files and those manually calculated was found to be less than 2%. Conclusion: An efficient and easy tool to perform routine QA procedure of EDW is suggested. The method can be easily implemented in any institution without a need for expensive QA equipment. An error of the order of ≥2% can be easily detected.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-76: Total Skin Electron Therapy: An-End-To-End Examination of the Absolute Dosimetry with a Rando Phantom

Purpose: To examine and validate the absolute dose for total skin electron therapy (TSET) through an end-to-end test with a Rando phantom using optically stimulated luminescent dosimeters (OSLDs) and EBT3 radiochromic films. Methods: A Varian Trilogy linear accelerator equipped with the special procedure 6 MeV HDTSe- was used to perform TSET irradiations using a modified Stanford 6-dual-field technique. The absolute dose was calibrated using a Markus ion chamber at a reference depth of 1.3cm at 100 cm SSD with a field size of 36 × 36 cm at the isocenter in solid water slabs. The absolute dose was cross validated by a farmer ion chamber. Then the dose rate in the unit of cGy/Mu was calibrated using the Markus chamber at the treatment position. OSLDs were used to independently verify the dose using the calibrated dose rate. Finally, a patient treatment plan (200 cGy/cycle) was delivered in the QA mode to a Rando phantom, which had 16 pairs of OSLDs and EBT3 films taped onto its surface at different anatomical positions. The doses recorded were read out to validate the absolute dosimetry for TSET. Results: The OSLD measurements were within 7% agreement with the planned dose except the shoulder areas, where the doses recorded were 23% lower on average than those of the planned. The EBT3 film measurements were within 10% agreement with the planned dose except the shoulder and the scalp vertex areas, where the respective doses recorded were 18% and 14% lower on average than those of the planned. The OSLDs gave more consistent dose measurements than those of the EBT3 films. Conclusion: The absolute dosimetry for TSET was validated by an end-to-end test with a Rando phantom using the OSLDs and EBT3 films. The beam calibration and monitor unit calculations were confirmed.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-J-144: Scatter and Leakage Survey of An Integrated MR-Linac System

Purpose: To assess the scatter and leakage radiation of an integrated 1.5T MRI-Linac system. Methods: A 150cc chamber (model 96020C, Inovision) was used in all the scatter and leakage measurements, after being recalibrated for MV energy by the Accredited Dosimetry Calibration Laboratory at MD Anderson. The scatter radiation was measured by placing a 25 cm stack of solid-water materials at iso-center on the patient couch to simulate patient scatter. Gantry angles were positioned at 0 degree (beam pointing downward) and 270 (beam pointing laterally). Scatter radiation was measured at selective locations inside the RF room. Beam stopper leakage was measured at the exterior panel of the gantry. The head leakage was measured at 1 meter away from the Linac head in the direction which was determined to be the area of maximum leakage by wrapped films test. All measurements were repeated with the 1.5T magnetic field turned off to study the effect of magnetic field. Results: When the magnet was on (B=1.5T), the maximum head leakage at 1 meter was 191.6mR/1000MU. The scatter radiation at 1 meter from the iso-center was 1.091R/1000MU when the radiation beam was pointing downward, 1.296R/1000MU when the beam pointed laterally. The beam stopper leakage was measured as 299.4 mR/1000MU at the exterior panel of the gantry. When magnet was off (B=0), the head leakage was measured as 198.6mR/1000MU. The scatter radiation at 1 meter was 1.153R/1000MU when beam pointed downward, 1.287R/1000MU when beam pointed laterally. The beam stopper leakage was measured as 309.4 mR/1000MU at the exterior panel of the gantry. Conclusion: The measurements indicate that the scatter and leakage radiation from the integrated MR-Linac system are in-line with the expected values. The beam stopper leakage is approximately 300 mR/1000MU. The leakage and scatter difference with the magnetic field ON and OFF was within 5%. The authors received a corporate sponsored grant from Elekta which is the vendor of the MR-Linac system studied in this work.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

TU-CD-304-01: FEATURED PRESENTATION and BEST IN PHYSICS (THERAPY): Trajectory Modulated Arc Therapy: Development of Novel Arc Delivery Techniques Integrating Dynamic Table Motion for Extended Volume Treatments

Purpose: Integration of coordinated robotic table motion with inversely-planned arc delivery has the potential to resolve table-top delivery limitations of large-field treatments such as Total Body Irradiation (TBI), Total Lymphoid Irradiation (TLI), and Cranial-Spinal Irradiation (CSI). We formulate the foundation for Trajectory Modulated Arc Therapy (TMAT), and using Varian Developer Mode capabilities, experimentally investigate its practical implementation for such techniques. Methods: A MATLAB algorithm was developed for inverse planning optimization of the table motion, MLC positions, and gantry motion under extended-SSD geometry. To maximize the effective field size, delivery trajectories for TMAT TBI were formed with the table rotated at 270° IEC and dropped vertically to 152.5cm SSD. Preliminary testing of algorithm parameters was done through retrospective planning analysis. Robotic delivery was programmed using custom XML scripting on the TrueBeam Developer Mode platform. Final dose was calculated using the Eclipse AAA algorithm. Initial verification of delivery accuracy was measured using OSLDs on a solid water phantom of varying thickness. Results: A comparison of DVH curves demonstrated that dynamic couch motion irradiation was sufficiently approximated by static control points spaced in intervals of less than 2cm. Optimized MLC motion decreased the average lung dose to 68.5% of the prescription dose. The programmed irradiation integrating coordinated table motion was deliverable on a TrueBeam STx linac in 6.7 min. With the couch translating under an open 10cmx20cm field angled at 10°, OSLD measurements along the midline of a solid water phantom at depths of 3, 5, and 9cm were within 3% of the TPS AAA algorithm with an average deviation of 1.2%. Conclusion: A treatment planning and delivery system for Trajectory Modulated Arc Therapy of extended volumes has been established and experimentally demonstrated for TBI. Extension to other treatment techniques such as TLI and CSI is readily achievable through the developed platform. Grant Funding by Varian Medical Systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

The OME Framework for genome-scale systems biology

The life sciences are undergoing continuous and accelerating integration with computational and engineering sciences. The biology that many in the field have been trained on may be hardly recognizable in ten to twenty years. One of the major drivers for this transformation is the blistering pace of advancements in DNA sequencing and synthesis. These advances have resulted in unprecedented amounts of new data, information, and knowledge. Many software tools have been developed to deal with aspects of this transformation and each is sorely needed. However, few of these tools have been forced to deal with the full complexity of genome-scale models along with high throughput genome-scale data. This particular situation represents a unique challenge, as it is simultaneously necessary to deal with the vast breadth of genome-scale models and the dizzying depth of high-throughput datasets. It has been observed time and again that as the pace of data generation continues to accelerate, the pace of analysis significantly lags behind. It is also evident that, given the plethora of databases and software efforts, it is still a significant challenge to work with genome-scale metabolic models, let alone next-generation whole cell models. We work at the forefront of model creation and systems scale data generation. The OME Framework was borne out of a practical need to enable genome-scale modeling and data analysis under a unified framework to drive the next generation of genome-scale biological models. Here we present the OME Framework. It exists as a set of Python classes. However, we want to emphasize the importance of the underlying design as an addition to the discussions on specifications of a digital cell. A great deal of work and valuable progress has been made by a number of communities towards interchange formats and implementations designed to achieve similar goals. While many software tools exist for handling genome-scale metabolic models or for genome-scale data analysis, no implementations exist that explicitly handle data and models concurrently. The OME Framework structures data in a connected loop with models and the components those models are composed of. This results in the first full, practical implementation of a framework that can enable genome-scale design-build-test. Over the coming years many more software packages will be developed and tools will necessarily change. However, we hope that the underlying designs shared here can help to inform the design of future software.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2

Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic’s evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (M pro ), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. Here, this work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic “warhead” to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of M pro with micromolar affinities (K I of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

Remotely Operated Equipment for Post Irradiation Examination of the SNS Target Vessel

The Spallation Neutron Source produces neutrons by accelerating protons into flowing mercury contained inside a stainless steel target vessel. During facility operation the target vessel is degraded by a combination of high-energy neutrons, the proton beam, and cavitation-induced corrosion. The degradation is primarily concentrated at the nose of the target vessel, where the proton beam passes through. Currently, the Spallation Neutron Source has replaced three target vessels and is operating the fourth. To minimize the operational costs of manufacturing and disposing of target vessels, efforts are underway to increase the operational lifetimes of the target vessels by conducting post irradiation examinations of spent vessels. This examination involves remotely removing multiple coupons from the nose of the target vessel using a single piece of equipment, called the Nose Sampling Cutter, installed inside the Spallation Neutron Source s hot cell. The Cutter produces circular coupons approximately 2 inches in diameter using a carbide-tipped hole saw. The nose of the target vessel consists of four layers of material, and the Nose Sampling Cutter is capable of cutting through the layers in a single stroke. This remote operation has been successfully completed twice. In addition to the Nose Sampling Cutter, a large reciprocation saw capable of removing a sizable section of the nose of the target vessel has been constructed and tested, but never implemented. To support this large reciprocation saw other equipment has also been designed. The details of the Nose Sampling Cutter, reciprocation saw, and associated equipment are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2016

SU-D-206-02: Evaluation of Partial Storage of the System Matrix for Cone Beam Computed Tomography Using a GPU Platform

Purpose: Iterative reconstruction algorithms in computed tomography (CT) require a fast method for computing the intersections between the photons’ trajectories and the object, also called ray-tracing or system matrix computation. This work evaluates different ways to store the system matrix, aiming to reconstruct dense image grids in reasonable time. Methods: We propose an optimized implementation of the Siddon’s algorithm using graphics processing units (GPUs) with a novel data storage scheme. The algorithm computes a part of the system matrix on demand, typically, for one projection angle. The proposed method was enhanced with accelerating options: storage of larger subsets of the system matrix, systematic reuse of data via geometric symmetries, an arithmetic-rich parallel code and code configuration via machine learning. It was tested on geometries mimicking a cone beam CT acquisition of a human head. To realistically assess the execution time, the ray-tracing routines were integrated into a regularized Poisson-based reconstruction algorithm. The proposed scheme was also compared to a different approach, where the system matrix is fully pre-computed and loaded at reconstruction time. Results: Fast ray-tracing of realistic acquisition geometries, which often lack spatial symmetry properties, was enabled via the proposed method. Ray-tracing interleaved with projection and backprojection operations required significant additional time. In most cases, ray-tracing was shown to use about 66 % of the total reconstruction time. In absolute terms, tracing times varied from 3.6 s to 7.5 min, depending on the problem size. The presence of geometrical symmetries allowed for non-negligible ray-tracing and reconstruction time reduction. Arithmetic-rich parallel code and machine learning permitted a modest reconstruction time reduction, in the order of 1 %. Conclusion: Partial system matrix storage permitted the reconstruction of higher 3D image grid sizes and larger projection datasets at the cost of additional time, when compared to the fully pre-computed approach. This work was supported in part by the Fonds de recherche du Quebec - Nature et technologies (FRQ-NT). The authors acknowledge partial support by the CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council of Canada (Grant No. 432290).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

VMAT QA: Measurement-guided 4D dose reconstruction on a patient

Purpose: To develop and validate a volume-modulated arc therapy (VMAT) quality assurance (QA) tool that takes as input a time-resolved, low-density ({approx}10 mm) cylindrical surface dose map from a commercial helical diode array, and outputs a high density, volumetric, time-resolved dose matrix on an arbitrary patient dataset. This first validation study is limited to a homogeneous 'patient.'Methods: A VMAT treatment is delivered to a diode array phantom (ARCCHECK, Sun Nuclear Corp., Melbourne, FL). 3DVH software (Sun Nuclear) derives the high-density volumetric dose using measurement-guided dose reconstruction (MGDR). MGDR cylindrical phantom results are then used to perturb the three-dimensional (3D) treatment planning dose on the patient dataset, producing a semiempirical volumetric dose grid. Four-dimensional (4D) dose reconstruction on the patient is also possible by morphing individual sub-beam doses instead of the composite. For conventional (3D) dose comparison two methods were developed, using the four plans (Multi-Target, C-shape, Mock Prostate, and Head and Neck), including their structures and objectives, from the AAPM TG-119 report. First, 3DVH and treatment planning system (TPS) cumulative point doses were compared to ion chamber in a cube water-equivalent phantom ('patient'). The shape of the phantom is different from the ARCCHECK and furthermore the targets were placed asymmetrically. Second, coronal and sagittal absolute film dose distributions in the cube were compared with 3DVH and TPS. For time-resolved (4D) comparisons, three tests were performed. First, volumetric dose differences were calculated between the 3D MGDR and cumulative time-resolved patient (4D MGDR) dose at the end of delivery, where they ideally should be identical. Second, time-resolved (10 Hz sampling rate) ion chamber doses were compared to cumulative point dose vs time curves from 4D MGDR. Finally, accelerator output was varied to assess the linearity of the 4D MGDR with global fluence change. Results: Across four TG-119 plans, the average PTV point dose difference in the cube between 3DVH and ion chamber is 0.1 {+-} 1.0%. Average film vs TPS {gamma}-analysis passing rates are 83.0%, 91.1%, and 98.4% for 1%/2 mm, 2%/2 mm, and 3%/3 mm threshold combinations, respectively, while average film vs 3DVH {gamma}-analysis passing rates are 88.6%, 96.1%, and 99.5% for the same respective criteria. 4D MGDR was also sufficiently accurate. First, for 99.5% voxels in each case, the doses from 3D and 4D MGDR at the end of delivery agree within 0.5%local dose-error/1 mm distance. Moreover, all failing voxels are confined to the edge of the cylindrical reconstruction volume. Second, dose vs time curves track between the ion chamber and 4D MGDR within 1%. Finally, 4D MGDR dose changes linearly with the accelerator output: the difference between cumulative ion chamber and MGDR dose changed by no more than 1% (randomly) with the output variation range of 10%. Conclusions: Even for a well-commissioned TPS, comparison metrics show better agreement on average to MGDR than to TPS on the arbitrary-shaped measurable 'patient.' The method requires no more accelerator time than standard QA, while producing more clinically relevant information. Validation in a heterogeneous thoracic phantom is under way, as is the ultimate application of 4D MGDR to virtual motion studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-10: Validation of ELP Dosimetry Using PRESAGE Dosimeter: Feasibility Test and Practical Considerations

Purpose: To validate the use of a PRESAGE dosimeter as a method to quantitatively measure dose distributions of injectable brachytherapy based on elastin-like polypeptide (ELP) nanoparticles. PRESAGE is a solid, transparent polyurethane-based dosimeter whose dose is proportional to a change in optical density, making it useful for visualizing the dose from a radionuclide-tagged-ELP injection. Methods: A PRESAGE dosimeter was designed to simulate an ELP injection. To calibrate, cuvette samples from the batch of PRESAGE were exposed to varying levels of radiation from 0–35.9Gy applied via a linear accelerator, then placed into a spectrophotometer to obtain the optical density change as a function of dose. A pre-optical-CT scan was acquired of the phantom to obtain a baseline tomographic optical density. A 1cc saline solution of I-125 tagged-ELP with and activity concentration of 1mCi/cc was injected into the phantom and left for five days. After five days, the ELP was removed and the cavity cleaned of all remaining radioactive material. Post tomographic optical images were acquired to obtain a differential optical density dataset. Results: Initial results after the 5-day exposure revealed an opaque white film that resembled the volume of the ELP solution injected into the phantom. We think this is possibly due to the saline solution diffusing into the PRESAGE and causing a change in the index of refraction at this shallow depth. Therefore, initially the optical scanner yielded inconclusive results. After several more days, the saline seemed to have evaporated out of the injection site and the ELP dose distribution was visible via color change in the dosimeter. Conclusion: We have created the first experimental design to measure the dose distribution of I-125-tagged-ELP. The PRESAGE formulation proves to be a feasible option for such measurements. Future experimental measurements need to be obtained to further characterize ELP dosimetry.

60 APPLIED LIFE SCIENCES↗