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DOE OSTI2016

MO-FG-202-08: Real-Time Monte Carlo-Based Treatment Dose Reconstruction and Monitoring for Radiotherapy

Purpose: This proof-of-concept study is to develop a real-time Monte Carlo (MC) based treatment-dose reconstruction and monitoring system for radiotherapy, especially for the treatments with complicated delivery, to catch treatment delivery errors at the earliest possible opportunity and interrupt the treatment only when an unacceptable dosimetric deviation from our expectation occurs. Methods: First an offline scheme is launched to pre-calculate the expected dose from the treatment plan, used as ground truth for real-time monitoring later. Then an online scheme with three concurrent threads is launched while treatment delivering, to reconstruct and monitor the patient dose in a temporally resolved fashion in real-time. Thread T1 acquires machine status every 20 ms to calculate and accumulate fluence map (FM). Once our accumulation threshold is reached, T1 transfers the FM to T2 for dose reconstruction ad starts to accumulate a new FM. A GPU-based MC dose calculation is performed on T2 when MC dose engine is ready and a new FM is available. The reconstructed instantaneous dose is directed to T3 for dose accumulation and real-time visualization. Multiple dose metrics (e.g. maximum and mean dose for targets and organs) are calculated from the current accumulated dose and compared with the pre-calculated expected values. Once the discrepancies go beyond our tolerance, an error message will be send to interrupt the treatment delivery. Results: A VMAT Head-and-neck patient case was used to test the performance of our system. Real-time machine status acquisition was simulated here. The differences between the actual dose metrics and the expected ones were 0.06%–0.36%, indicating an accurate delivery. ∼10Hz frequency of dose reconstruction and monitoring was achieved, with 287.94s online computation time compared to 287.84s treatment delivery time. Conclusion: Our study has demonstrated the feasibility of computing a dose distribution in a temporally resolved fashion in real-time and quantitatively and dosimetrically monitoring the treatment delivery.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Evaluation of OpenAI Codex for HPC Parallel Programming Models Kernel Generation

We evaluate AI-assisted generative capabilities on fundamental numerical kernels in high-performance computing (HPC), including AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG. We test the generated kernel codes for a variety of language-supported programming models, including (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numpy, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). We use the GitHub Copilot capabilities powered by the GPT-based OpenAI Codex available in Visual Studio Code as of April 2023 to generate a vast amount of implementations given simple + + prompt variants. To quantify and compare the results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. Results suggest that the OpenAI Codex outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general purpose Python can benefit from adding code keywords, while Julia prompts perform acceptably well for its mature programming models (e.g., Threads and CUDA.jl). We expect for these benchmarks to provide a point of reference for each programming model's community. Overall, understanding the convergence of large language models, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.

Godoy, William↗

DOE OSTI2023

Enhanced lightning strike protection using vertically oriented carbon fiber melded with conventional carbon fiber-reinforced composite and its validation through damage analysis

Lightning strike protection (LSP) is one of the prime factors in aerospace and wind industries concerning safety, enhanced service life, and reduced downtime. To ensure better LSP, high electrical conductivity is required to dissipate the current, which is always a challenge for polymer composites due to the inherent insulating nature of the polymer matrix. Conventional carbon fiber-reinforced composites (CFRP) offer electrical conductivity in the planar direction while the vertical i.e. through-thickness conductivity still remains a challenge. Having been motivated by this fact, we have fabricated CFRP interleaved with vertically oriented CF (Z-fiber) for the lightning strike test (100 kA). A paint was applied to mimic the actual service condition of the composite laminates. We have prepared two Z-fiber composites: (a) Z-1 containing one Z-fiber layer on the top along with conventional CF layers and (b) Z-5 containing five interleaved Z-fiber layers and compared the properties with conventional CFRP (Z-0). Interestingly, even a single Z-fiber layer (Z-1) showed lower damage (visual damage diameter 22 mm) than Z-0 (visual damage diameter 26 mm). Z-5 displayed the lowest damage (visual damage diameter 16.7 mm), which was further confirmed by cross-sectional optical microscopy. Improved LSP was attributed to the higher through-thickness electrical conductivity in the case of Z-5 (9 times with respect to Z-0) reflecting a lower electrical anisotropy for Z-fiber composites. The residual mechanical property after the lightning test was analyzed through the flexural test, and the retention of flexural strength and modulus was 66% and 86%, respectively for Z-5 showing a significant improvement in comparison to Z-0 (>40% for both).

Saha, Subhabrata↗

DOE OSTI2016

CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. Cis SERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. Cis SERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, Cis SERS utilizes the REBASE enzyme database. Results from Cis SERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. Cis SERS is a java based graphical user interface built around a perl backbone. Several of the applications of Cis SERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool Cis SERSand results from in-silico and corresponding wet-lab analyses demonstrating that Cis SERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Comparison of ML-Based Proxy Modeling Strategies: Lessons Learned from the SMART Initiative

Teams of researchers on Task 5 of the SMART project have developed a variety of modeling architectures to predict subsurface behavior during carbon injection and post-injection periods. One important part of this task was to compare the candidate approaches in terms of accuracy, reliability, speed, and memory use, all using a common set of metrics and visualizations for an “apples to apples” comparison. Dr. Jared Schuetter will share the details of this task, the results that were obtained, and the lessons learned.

Schuetter, Jared↗

DOE OSTI2016

DYNAMIC SPECTRAL MAPPING OF INTERSTELLAR PLASMA LENSES

Compact radio sources sometimes exhibit intervals of large, rapid changes in their flux density, due to lensing by interstellar plasma crossing the line of sight. A novel survey program has made it possible to discover these “Extreme Scattering Events” (ESEs) in real time, resulting in a high-quality dynamic spectrum of an ESE observed in PKS 1939–315. Here we present a method for determining the column-density profile of a plasma lens, given only the dynamic radio spectrum of the lensed source, under the assumption that the lens is either axisymmetric or totally anisotropic. Our technique relies on the known, strong frequency dependence of the plasma refractive index in order to determine how points in the dynamic spectrum map to positions on the lens. We apply our method to high-frequency (4.2–10.8 GHz) data from the Australia Telescope Compact Array of the PKS 1939–315 ESE. The derived electron column-density profiles are very similar for the two geometries we consider, and both yield a good visual match to the data. However, the fit residuals are substantially above the noise level, and deficiencies are evident when we compare the predictions of our model to lower-frequency (1.6–3.1 GHz) data on the same ESE, thus motivating future development of more sophisticated inversion techniques.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1976

The use of spatial characteristics for the improvement of multispectral classification of remotely sensed data

Two techniques for the classification of multispectral remotely sensed data - the image processing technique of texture features, which is modeled after the human visual system, and the ECHO (Extraction and Classification of Homogeneous Objects) numerical technique - are examined. These two spatial analysis techniques are compared using Landsat imagery of an area of Indiana as an example, and it is found that the numerical approach is superior in classification accuracy and more efficient computationally.

Wiersma, D. J.↗

NASA NTRS1980

Investigations of eddy coherence in jet flows

In turbulent shear flow the term coherent structures refers to eddies which are both spatially coherent, i.e., large eddies, aand also temporally coherent, i.e., they retain their identities for times which are long compared with their time scales in fixed point measurements. In transitional flows, the existence of such structures is evident from flow visualizations. In many other flows, such structures are not so evident. The reasons for the existence of these two classes of flows are discussed and attention is focused upon the more difficult flows, where coherent structures are not so evident. Techniques by which the existence (or nonexistence) of such structures in these flows can be established from point measurements, are also discussed. A major problem is shown to be the need to discriminate between real losses in eddy coherence and apparent losses in coherence introduced by phase scrambling effects which 'smear' multipoint correlations. The analysis of multiprobe time dependent data in cold and reacting round turbulent jets is described and it is shown how evidence of strong eddy coherence can be extracted from data.

Yule, A. J.↗

NASA NTRS1982

Optical polarization of the Seyfert galaxies IC 4329A and MRK 376

Measurements of the optical polarizations of the two highly polarized Seyfert 1 galaxies IC 4329A and Mrk 376 are presented. Continuum and line polarization of the two objects were observed with the Steward Observatory 2.25-m telescope using a two-channel photoelectric Pockels cell polarimeter, a single-channel scanner, and a digicon attached to a flint prism spectrograph. Results indicate that, for both galaxies, the emission line polarization and underlying continuum polarization are identical, rising toward short wavelengths, and therefore must be explained by a common mechanism. Such a mechanism is suggested to involve polarization produced by aligned grains in the galactic disk. A model for polarization in IC 4329A by this mechanism predicts a grain size three times smaller than Galactic polarizing grains, as well as a visual extinction of about 2 magnitudes, a gas to dust mass ratio close to 100 and a polarization to extinction ratio comparable to the Galactic ratio.

Martin, P. G.↗

NASA NTRS1982

Interpretation of remotely sensed data and its applications in oceanography

The methodology of interpretation of remote sensing data and its oceanographic applications are described. The elements of image interpretation for different types of sensors are discussed. The sensors utilized are the multispectral scanner of LANDSAT, and the thermal infrared of NOAA and geostationary satellites. Visual and automatic data interpretation in studies of pollution, the Brazil current system, and upwelling along the southeastern Brazilian coast are compared.

Parada, N. D. J.↗

NASA NTRS1983

Comparison of simulator fidelity model predictions with in-simulator evaluation data

A full factorial in simulator experiment of a single axis, multiloop, compensatory pitch tracking task is described. The experiment was conducted to provide data to validate extensions to an analytic, closed loop model of a real time digital simulation facility. The results of the experiment encompassing various simulation fidelity factors, such as visual delay, digital integration algorithms, computer iteration rates, control loading bandwidths and proprioceptive cues, and g-seat kinesthetic cues, are compared with predictions obtained from the analytic model incorporating an optimal control model of the human pilot. The in-simulator results demonstrate more sensitivity to the g-seat and to the control loader conditions than were predicted by the model. However, the model predictions are generally upheld, although the predicted magnitudes of the states and of the error terms are sometimes off considerably. Of particular concern is the large sensitivity difference for one control loader condition, as well as the model/in-simulator mismatch in the magnitude of the plant states when the other states match.

Parrish, R. V.↗

NASA NTRS1987

A study of multi-body aerodynamic interference at transonic Mach numbers

A wind tunnel experiment involving single, double, and triple combinations of mutually interfering generic, unfinned aircraft stores has been conducted. Each combination of stores was tested at Mach numbers from 0.60 to 1.20 and at angles of attack from 0 to 25 deg for the single store and from 0 to 6 deg for the double and triple store configurations. Extensive axial and circumferential pressure and flow visualization data at each store location were obtained. Euler solutions for each configuration at 0 deg incidence have been generated and compared with experimental data. This comparison indicates an Euler flow solver can yield accurate predictions of the location and magnitude of multibody interference provided an appropriate grid is used and the viscous effects associated with these configurations remain small. The data indicate multibody interference in the transonic region increases as the freestream Mach number approaches 1 from either direction, and subsides as the Mach number moves away from sonic conditions. This interference is characterized by a large, localized reduction in pressure on the inboard surfaces of the bodies which results in forces that draw the configuration closer together.

Cottrell, Charles J.↗

NASA NTRS1989

Thermocapillary migration of liquid droplets in a temperature gradient in a density matched system

An experimental investigation of thermocapillary flow in droplets of a vegetable oil (partially hydrogenated soybean oil) immersed in silicone oil was conducted in a test cell with a heated top wall and a cooled bottom wall. The liquids are nearly immiscible and have equal densities at a temperature below the room temperature, thus providing a simulation of low-gravity conditions by reducing the buoyancy forces. The interfacial tension between the two oils was measured in the temperature range 20 to 50 C using a capillary tube and (d sigma)/(d T) was determined to be negative. Droplets ranging in sizes from 3 mm to 1 cm diameter were injected into the silicone oil. The vertical temperature profile in the bulk liquid (silicone oil) produces temperature variations along the interface which induce variations in the interfacial tension. The flow inside the droplet driven by the resulting interfacial shear stresses was observed using a laser light-sheet flow visualization technique. The flow direction is consistent with the sign of (d sigma)/(d T). The observed maximum surface velocities are compared to the theoretical predictions of Young et al. (1959).

Rashidnia, N.↗

NASA NTRS1991

Thermocapillary migration of liquid droplets in a temperature gradient in a density matched system

Rashidnia, N.↗

NASA NTRS2003

Hot Views on Cold Crystals: The Application of Thermal Imaging in Cryocrystallography

We have used thermal imaging techniques to visualize the cryocooling processes of macromolecular crystals. Cryocooling is a common technique used for structural data collection to reduce radiation damage in intense X-ray beams and decrease the thermal motion of the atoms. From the thermal images it was clear that during cryocooling a cold wave progresses through a crystal starting at the face closest to the origin of the cold stream and ending at the point furthest away. As an extension to this work, we used thermal imaging to study small crystals, held in a cryo-loop, in the presence of vitrified mother liquor. The different infrared transmission and reflectance properties of the crystal in comparison to the mother liquor surrounding it are thought to be the parameter that produces the contrast that makes the crystal visible. An application of this technology may be the determination of the exact location of small crystals in a cryo-loop for automated structural genomics studies. Data from initial tests in support of application development was recorded for lysozyme crystals and for bFGF/dna complex crystals, which were cryocooled and imaged in large loops, both with visible light and with infrared radiation. The crystals were clearly distinguished from the vitrified solution in the infrared spectrum, while in the case of the bFGF/dna complex the illumination had to be carefully manipulated to make the crystal visible in the visible spectrum. These results suggest that the thermal imaging may be more sensitive than visual imaging for automated location of small crystals. However, further work on small crystals robotically mounted at SSRL did not clearly visualize those crystals. The depth of field of the camera proved to be limiting and a different cooling geometry was used, compared to the previous, successful experiments. Analysis to exploit multiple images to improve depth of field and experimental work to understand cooling geometry effects is ongoing. These results will be presented along with advantages and disadvantages of the technique and a discussion of how it might be applied.

Snell, Eddie↗

NASA NTRS2003

Hot Views on Cold Crystals: The Application of Thermal Imaging in Cryocrystallography

In the past we have used thermal imaging techniques to visualize the cryocooling processes of macromolecular crystals. From these images it was clear that a cold wave progresses through a crystal starting at the face closest to the origin of the cold stream and ending at the point furthest away. During these studies we used large volume crystals, which were clearly distinguished from the loop holding them. These large crystals, originally grown for neutron diffraction studies, were chosen deliberately to enhance the imaging. As an extension to this work, we used thermal imaging to study small crystals, held in a cryo- loop, in the presence of vitrified mother liquor. The different infrared transmission and reflectance properties of the crystal in comparison to the mother liquor surrounding it are thought to be the parameter that produces the contrast that makes the crystal visible. An application of this technology may be the determination of the exact location of small crystals in a cryo-loop. Data from initial tests in support of application development was recorded for lysozyme crystals and for bFGF/dna complex crystals, which were cryo-cooled and imaged in large loops, both with visible light and with infrared radiation. The crystals were clearly distinguished from the vitrified solution in the infrared spectrum, while in the case of the bFGF/dna complex the illumination had to be carefully manipulated to make the crystal visible in the visible spectrum. These results suggest that the thermal imaging may be more sensitive than visual imaging for automated location of small crystals. However, further work on small crystals robotically mounted at SSRL did not clearly visualize those crystals. The depth of field of the camera proved to be limiting and a different cooling geometry was used, compared to the previous, successful experiments. Analysis to exploit multiple images to improve depth of field and experimental work to understand cooling geometry effects is ongoing. These results will be presented along with advantages and disadvantages of the technique and a discussion of how it might be applied .

Snell, Eddie H.↗

NASA NTRS2003

Hot Views on Cold Crystals: The Application of Thermal Imaging in Cryo-crystallography

In the past we have used thermal imaging techniques to visualize the cryocooling processes of macromolecular crystals. From these images it was clear that a cold wave progresses through a crystal starting at the face closest to the origin of the cold stream and ending at the point furthest away. During these studies we used large volume crystals, which were clearly distinguished from the loop holding them. These large crystals, originally grown for neutron diffraction studies, were chosen deliberately to enhance the imaging. As an extension to this work, we present used thermal imaging to study small crystals, held in a cryo-loop, in the presence of vitrified mother liquor. The different infrared transmission and reflectance properties of the crystal in comparison to the mother liquor surrounding it are thought to be the parameter that produces the contrast that makes the crystal visible. An application of this technology may be the determination of the exact location of small crystals in a cryo-loop. Data from initial tests in support of application development was recorded for lysozyme crystals and for bFGF/dna complex crystals, which were cryo-cooled and imaged in large loops, both with visible light and with infrared radiation. The crystals were clearly distinguished from the vitrified solution in the infrared spectrum, while in the case of the bFGF/dna complex the illumination had to be carefully manipulated to make the crystal visible in the visible spectrum. These results suggest that the thermal imaging may be more sensitive than visual imaging for automated location of small crystals. However, further work on small crystals robotically mounted at SSRL did not clearly visualize those crystals. The depth of field of the camera proved to be limiting and a different cooling geometry was used, compared to the previous, successful experiments. Analysis to exploit multiple images to improve depth of field and experimental work to understand cooling geometry effects is ongoing. These results will be presented along with advantages and disadvantages of the technique and a discussion of how it might be applied.

Snell, E. H.↗

NASA NTRS2004

Hot Stuff? Thermal Imaging Applied to Cryocrystallography

In the past we have used thermal imaging techniques to visualize the cryocooling processes of macromolecular crystals. From these images it was clear that a cold wave progresses through a crystal starting at the face closest to the origin of the cold stream and ending at the point furthest away. During these studies we used large volume crystals, which were clearly distinguished fiom the loop holding them. These large crystals, originally grown for neutron diffiaction studies, were chosen deliberately to enhance the imaging. As an extension to this work, we present used thermal imaging to study small crystals, held in a cryo-loop, in the presence of vitrified mother liquor. The different d a r e d transmission and reflectance properties of the crystal in comparison to the mother liquor surrounding it are thought to be the parameter that produces the contrast that makes the crystal visible. An application of this technology may be the determination of the exact location of small crystals in a cryo-loop. Data fkom initial tests in support of application development was recorded for lysozyme crystals and for bFGF/dna complex crystals, which were cryocooled and imaged in large loops, both with visible light mad with h i k e d rdi&tion. The crystals were clearly distinguished from the vitrified solution in the infiared spectrum, while in the case of the bFGF/dna complex the illumination had to be carefully manipulated to make the crystal visible in the visible spectrum. These results suggest that the thermal imaging may be more sensitive than visual imaging for automated location of small crystals. However, further work on small crystals robotically mounted at SSRL did not clearly visualize those crystals. The depth of field of the camera proved to be limiting and a different cooling geometry was used, compared to the previous, successful experiments. Analysis to exploit multiple images to improve depth of field and experimental work to understand cooling geometry effects is ongoing. These results will be presented along with advantages and disadvantages of the technique and a discussion of how it might be applied.

Snell, E. H.↗