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NASA NTRS2024

Comparison of Geant4-DNA and RITRACKS/RITCARD: Microdosimetry, Nanodosimetry and DNA Damage Predictions for Low to High LET Ions

Low linear energy transfer (LET) ionizing radiations induce homogeneously distributed DNA damage at the cellular scale, while high LET ionizing radiations are well known to create complex biological damage including clustered double strand breaks (DSB). Clustered DSB are critical events that are difficult to repair, leading to increased biological outcomes compared to low LET radiation exposure. Recent studies have shown that DNA compaction, which can be actively modified by the cell to allow DNA repair, influences the yield of DSB [1]. The goal of this work is to determine the impact of DNA compaction on chromosome aberration formation, a biomarker of radiation-induced cancer risk. The RITRACKS track structure code [2], together with the RITCARD code [3], allow one to simulate the transport of high LET ions, calculate DNA damage and repair, and chromosome aberration formation, but does not include detailed geometrical models of DNA. The Geant4-DNA toolkit provides such detailed models with different levels of DNA compaction [1,4], but does not model chromosome aberration formation. In this work, these highly detailed DNA geometries are used to compute DNA breaks with Geant4-DNA and combine the results with the RITCARD tool to compute chromosome aberrations. As a first step, we compared the transport models used in RITRACKS and Geant4-DNA and newly released heavy ion model transport (G4DNARuddIonisationExtendedModel Geant4 v11.2) to ensure consistency between the physical stage of the two radiation transport codes. We compared energy deposition at the micrometric and nanometric scales for different ions (H 250 MeV, H 150 Me, He 250 MeV/n, C 290 MeV/n, O 350 MeV/n, O 55 MeV/n, Si 170MeV/n, Ti 300 MeV/n, Ti 300 MeV/n, Fe 600 MeV/n, Fe 450 MeV/n and Fe 300 MeV/n) with LET ranging from ~0.4 keV/μm up to 235 keV/μm. Excellent agreement is found for both microdosimetric and nanodosimetric spectra for all ion types and energies. The calculation of DNA breaks and their complexity with the Geant4-DNA is an ongoing work, and comparison with RITCARD will be presented based on result availability at the time of the conference. [1] Tang et al. (2019). Med. Phys., 46(3), 1501-1511. [2] Plante et al. (2008). NJP, 10(12), 125020. [3] Plante et al. (2019). Rad. Res., 192(3), 282-298. [4] Incerti et al. (2018). Med. Phys., 45(8), e722-e739.

Floriane Poignant↗

NASA NTRS2021

Revisiting Topographic Horizons in the Era of Big Data and Parallel Computing

Widely used to calculate illumination geometry forestimates of solar and emitted longwave radiation, and forcorrecting remotely sensed data for topographic effects, digitalelevation models (DEMs) are now extensive globally at 10–30-mspatial resolution and locally at spatial resolutions down to afew centimeters. Globally, regionally, or locally, elevation datasetshave many grid points. Many software packages calculate gradi-ents over every grid cell or point, but in the mountains, shadingby nearby terrain must also be assessed. Terrain may obscure aslope that would otherwise face the Sun. Four decadesago, a fastmethod to calculate topographic horizons at every point in anelevation grid required computations related only linearly to thesize of the grid, but grids now have so many points that parallelcomputing still provides an advantage. Exploiting parallelismover terrain grids can use alternative strategies: among columnsof a rotated grid, or simultaneously at multiple rotation angles,or on different tiles of a grid. On a multi-processor machine, theimprovement in computing time approaches 2/3 the number ofprocessors deployed,

Jeff Dozier↗

NASA NTRS1990

Parametric analysis of swept-wing geometry with sheared wing tips

A computational parameter study is presented of potential reductions in induced drag and increases in lateral-directional stability due to sheared wing tips attached to an untwisted wing of moderate sweep and aspect ratio. Sheared tips are swept and tapered wing-tip devices mounted in the plane of the wing. The induced-drag results are obtained using an inviscid, incompressible surface-panel method that models the nonlinear effects due to the deflected and rolled-up wake behind the lifting surface. The induced-drag results with planar sheared tips are compared to straight-tapered tip extensions and nonplanar winglet geometries. The lateral-directional static-stability characteristics of the wing with sheared tips are estimated using a quasi-vortex-lattice method. For certain combinations of sheared-tip sweep and taper, both the induced efficiency of the wing and the relevant static-stability derivatives are predicted to increase compared to the wing with a straight-tapered tip modification.

Fremaux, C. M.↗

NASA NTRS1989

The effect of ionization on the infrared absorption spectra of PAHs: A preliminary report

The emission lines observed in many interstellar IR sources at 3.28, 6.2, 7.7, 8.7, and 11.3 microns are theorized to originate from polycyclic aromatic hydrocarbons (PAHs). These assignments are based on analyses of lab IR spectra of neutral PAHs. However, it is likely that in the interstellar medium that PAHs are ionized, i.e., are positively charged. Besides, as pointed out by Allamandola et al., although the IR emission band spectrum resembles what one might expect from a mixture of PAHs, it does not match in details such as frequency, band profile, or relative intensities predicted from the absorption spectra of any known PAH molecule. One source of more information to test the PAH theory is ab initio molecular orbital theory. It can be used to compute, from first principles, the geometries, vibrational frequencies, and vibrational intensities for model PAH compounds which are difficult to study in the lab. The Gaussian 86 computer program was used to determine the effect of ionization on the infrared absorption spectra of several small PAHs: naphthalene and anthracene. A preliminary report is presented of the results of these calculations.

Defrees, Doug J.↗

NASA NTRS2014

A Formally-Verified Decision Procedure for Univariate Polynomial Computation Based on Sturm's Theorem

Sturm's Theorem is a well-known result in real algebraic geometry that provides a function that computes the number of roots of a univariate polynomial in a semiopen interval. This paper presents a formalization of this theorem in the PVS theorem prover, as well as a decision procedure that checks whether a polynomial is always positive, nonnegative, nonzero, negative, or nonpositive on any input interval. The soundness and completeness of the decision procedure is proven in PVS. The procedure and its correctness properties enable the implementation of a PVS strategy for automatically proving existential and universal univariate polynomial inequalities. Since the decision procedure is formally verified in PVS, the soundness of the strategy depends solely on the internal logic of PVS rather than on an external oracle. The procedure itself uses a combination of Sturm's Theorem, an interval bisection procedure, and the fact that a polynomial with exactly one root in a bounded interval is always nonnegative on that interval if and only if it is nonnegative at both endpoints.

Narkawicz, Anthony J.↗

DOE OSTI2021

PCalc User's Manual

PCalc is a software tool that computes travel-time predictions, ray path geometry and model queries. This software has a rich set of features, including the ability to use custom 3D velocity models to compute predictions using a variety of geometries. The PCalc software is especially useful for research related to seismic monitoring applications.

58 GEOSCIENCES↗

DOE OSTI2024

Performance Analysis of an Optimization Algorithm for Metamaterial Design on the Integrated High-Performance Computing and Quantum Systems

Optimizing metamaterials with complex geometries is a big challenge. Although an active learning algorithm, combining machine learning (ML), quantum computing, and optical simulation, has emerged as an efficient optimization tool, it still faces difficulties in optimizing complex structures that have potentially high performance. In this work, we comprehensively analyze the performance of an optimization algorithm for metamaterial design on the integrated HPC and quantum systems. We demonstrate significant time advantages through message-passing interface (MPI) parallelization on the high-performance computing (HPC) system showing approximately 54% faster ML tasks and 67 times faster optical simulation against serial workloads. Furthermore, we analyze the performance of a quantum algorithm designed for optimization, which runs with various quantum simulators on a local computer or HPC-quantum system. Results showcase ~24 times speedup when executing the optimization algorithm on the HPC-quantum hybrid system. This study paves a way to optimize complex metamaterials using the integrated HPC-quantum system.

Kim, Seongmin↗

NASA NTRS2001

Towards Accurate Prediction of Turbulent, Three-Dimensional, Recirculating Flows with the NCC

The National Combustion Code (NCC) was used to calculate the steady state, nonreacting flow field of a prototype Lean Direct Injection (LDI) swirler. This configuration used nine groups of eight holes drilled at a thirty-five degree angle to induce swirl. These nine groups created swirl in the same direction, or a corotating pattern. The static pressure drop across the holes was fixed at approximately four percent. Computations were performed on one quarter of the geometry, because the geometry is considered rotationally periodic every ninety degrees. The final computational grid used was approximately 2.26 million tetrahedral cells, and a cubic nonlinear k - epsilon model was used to model turbulence. The NCC results were then compared to time averaged Laser Doppler Velocimetry (LDV) data. The LDV measurements were performed on the full geometry, but four ninths of the geometry was measured. One-, two-, and three-dimensional representations of both flow fields are presented. The NCC computations compare both qualitatively and quantitatively well to the LDV data, but differences exist downstream. The comparison is encouraging, and shows that NCC can be used for future injector design studies. To improve the flow prediction accuracy of turbulent, three-dimensional, recirculating flow fields with the NCC, recommendations are given.

Iannetti, A.↗

NASA NTRS1989

The implementation of the graphics of program EAGLE: A numerical grid generation code on NASA Langley SNS computer system

Program EAGLE (Eglin Arbitrary Geometry Implicit Euler) Numerical Grid Generation System is a composite (multi-block) algebraic or elliptic grid generation system designed to discretize the domain in and/or around any arbitrarily shaped three dimensional regions. This system combines a boundary conforming surface generation scheme and includes plotting routines designed to take full advantage of the DISSPLA Graphics Package (Version 9.0). Program EAGLE is written to compile and execute efficiently on any Cray machine with or without solid state disk (SSD) devices. Also, the code uses namelist inputs which are supported by all Cray machines using the FORTRAN compiler CFT77. The namelist inputs makes it easier for the user to understand the inputs and operation of Program EAGLE. EAGLE's numerical grid generator is constructed in the following form: main program, EGG (executive routine); subroutine SURFAC (surface generation routine); subroutine GRID (grid generation routine); and subroutine GRDPLOT (grid plotting routines). The EAGLE code was modified to use on the NASA-LaRC SNS computer (Cray 2S) system. During the modification a conversion program was developed for the output data of EAGLE's subroutine GRID to permit the data to be graphically displayed by IRIS workstations, using Plot3D. The code of program EAGLE was modified to make operational subroutine GRDPLOT (using DI-3000 Graphics Software Packages) on the NASA-LaRC SNS Computer System. How to implement graphically, the output data of subroutine GRID was determined on any NASA-LaRC graphics terminal that has access to the SNS Computer System DI-300 Graphics Software Packages. A Quick Reference User Guide was developed for the use of program EAGLE on the NASA-LaRC SNS Computer System. One or more application program(s) was illustrated using program EAGLE on the NASA LaRC SNS Computer System, with emphasis on graphics illustrations.

Houston, Johnny L.↗

DOE OSTI2024

Source shape estimation for neutron imaging systems using convolutional neural networks

Neutron imaging systems are important diagnostic tools for characterizing the physics of inertial confinement fusion reactions at the National Ignition Facility (NIF). In particular, neutron images give diagnostic information on the size, symmetry, and shape of the fusion hot spot and surrounding cold fuel. Images are formed via collection of neutron flux from the source using a system of aperture arrays and scintillator-based detectors. Currently, reconstruction of fusion source geometry from the collected neutron images is accomplished by solving a computationally intensive maximum likelihood estimation problem via expectation maximization. In contrast, it is often useful to have simple representations of the overall source geometry that can be computed quickly. In this work, we develop convolutional neural networks (CNNs) to reconstruct the outer contours of simple source geometries. We compare the performance of the CNN for penumbral and pinhole data and provide experimental demonstrations of our methods on both non-noisy and noisy data.

Machine learning, neutron imaging, source reconstr↗

NASA NTRS1982

On composites with periodic structure

The overall moduli of a composite with an isotropic elastic matrix containing periodically distributed (anisotropic) inclusions or voids, can be expressed in terms of several infinite series which only depend on the geometry of the inclusions or voids, and hence can be computed once and for all for given geometries. For solids with periodic structures these infinite series play exactly the same role as does Eshelby's tensor for a single inclusion or void in an unbounded elastic medium. For spherical and circular-cylindrical geometries, the required infinite series are calculated and the results are tabulated. These are then used to estimate the overall elastic moduli when either the overall strains or the overall stresses are prescribed, obtaining the same results. These results are compared with other estimates and with experimental data. It is found that the model of composites with periodic structure yields estimates in excellent agreement with the experimental observations.

Nemat-Nasser, S.↗

NASA NTRS1993

Some useful innovations with TRASYS and SINDA-85

Several innovative methods were used to allow more efficient and accurate thermal analysis using SINDA-85 and TRASYS, including model integration and reduction, planetary surface calculations, and model animation. Integration with other modeling and analysis codes allows an analyst to import a geometry from a solid modeling or computer-aided design (CAD) software package, rather than building the geometry 'by hand.' This is more efficient as well as potentially more accurate. However, the use of solid modeling software often generates large analytical models. The problem of reducing large models was elegantly solved using the response of the transient derivative to a forcing step function. The thermal analysis of a lunar rover implemented two unusual features of the TRASYS/SINDA system. A little-known TRASYS routine SURFP calculates the solar heating of a rover on the lunar surface for several different rover positions and orientations. This is used not only to determine the rover temperatures, but also to automatically determine the power generated by the solar arrays. The animation of transient thermal results is an effective tool, especially in a vivid case such as the 14-day progress of the sun over the lunar rover. An animated color map on the solid model displays the progression of temperatures.

Amundsen, Ruth M.↗

NASA NTRS1993

Some Useful Innovations with Trasys and Sinda-85

Several innovative methods have been used to allow more efficient and accurate thermal analysis using SINDA-85 and TRASYS, including model integration and reduction, planetary surface calculations, and model animation. Integration with other modeling and analysis codes allows an analyst to import a geometry from a solid modeling or computer-aided design (CAD) software package, rather than building the geometry "by hand." This is more efficient as well as potentially more accurate. However, the use of solid modeling software often generates large analytical models. The problem of reducing large models has been elegantly solved using the response of the transient derivative to a forcing step function. The thermal analysis of a lunar rover implemented two unusual features of the TRASYS/SINDA system. A little-known TRASYS routine SURFP calculates the solar heating of a rover on the lunar surface for several different rover positions and orientations. This is used not only to determine the rover temperatures, but also to automatically determine the power generated by the solar arrays. The animation of transient thermal results is an effective tool, especially in a vivid case such as the 14-day progress of the sun over the lunar rover. An animated color map on the solid model displays the progression of temperatures.

Amundsen, Ruth M.↗

NASA NTRS2008

Spiking Neurons for Analysis of Patterns

Artificial neural networks comprising spiking neurons of a novel type have been conceived as improved pattern-analysis and pattern-recognition computational systems. These neurons are represented by a mathematical model denoted the state-variable model (SVM), which among other things, exploits a computational parallelism inherent in spiking-neuron geometry. Networks of SVM neurons offer advantages of speed and computational efficiency, relative to traditional artificial neural networks. The SVM also overcomes some of the limitations of prior spiking-neuron models. There are numerous potential pattern-recognition, tracking, and data-reduction (data preprocessing) applications for these SVM neural networks on Earth and in exploration of remote planets. Spiking neurons imitate biological neurons more closely than do the neurons of traditional artificial neural networks. A spiking neuron includes a central cell body (soma) surrounded by a tree-like interconnection network (dendrites). Spiking neurons are so named because they generate trains of output pulses (spikes) in response to inputs received from sensors or from other neurons. They gain their speed advantage over traditional neural networks by using the timing of individual spikes for computation, whereas traditional artificial neurons use averages of activity levels over time. Moreover, spiking neurons use the delays inherent in dendritic processing in order to efficiently encode the information content of incoming signals. Because traditional artificial neurons fail to capture this encoding, they have less processing capability, and so it is necessary to use more gates when implementing traditional artificial neurons in electronic circuitry. Such higher-order functions as dynamic tasking are effected by use of pools (collections) of spiking neurons interconnected by spike-transmitting fibers. The SVM includes adaptive thresholds and submodels of transport of ions (in imitation of such transport in biological neurons). These features enable the neurons to adapt their responses to high-rate inputs from sensors, and to adapt their firing thresholds to mitigate noise or effects of potential sensor failure. The mathematical derivation of the SVM starts from a prior model, known in the art as the point soma model, which captures all of the salient properties of neuronal response while keeping the computational cost low. The point-soma latency time is modified to be an exponentially decaying function of the strength of the applied potential. Choosing computational efficiency over biological fidelity, the dendrites surrounding a neuron are represented by simplified compartmental submodels and there are no dendritic spines. Updates to the dendritic potential, calcium-ion concentrations and conductances, and potassium-ion conductances are done by use of equations similar to those of the point soma. Diffusion processes in dendrites are modeled by averaging among nearest-neighbor compartments. Inputs to each of the dendritic compartments come from sensors. Alternatively or in addition, when an affected neuron is part of a pool, inputs can come from other spiking neurons. At present, SVM neural networks are implemented by computational simulation, using algorithms that encode the SVM and its submodels. However, it should be possible to implement these neural networks in hardware: The differential equations for the dendritic and cellular processes in the SVM model of spiking neurons map to equivalent circuits that can be implemented directly in analog very-large-scale integrated (VLSI) circuits.

Huntsberger, Terrance↗

NASA NTRS2011

Summary of the Tandem Cylinder Solutions from the Benchmark Problems for Airframe Noise Computations-I Workshop

Fifteen submissions in the tandem cylinders category of the First Workshop on Benchmark problems for Airframe Noise Computations are summarized. Although the geometry is relatively simple, the problem involves complex physics. Researchers employed various block-structured, overset, unstructured and embedded Cartesian grid techniques and considerable computational resources to simulate the flow. The solutions are compared against each other and experimental data from 2 facilities. Overall, the simulations captured the gross features of the flow, but resolving all the details which would be necessary to compute the noise remains challenging. In particular, how to best simulate the effects of the experimental transition strip, and the associated high Reynolds number effects, was unclear. Furthermore, capturing the spanwise variation proved difficult.

Lockard, David P.↗

NASA NTRSDate not supplied

Unsteady CFD Simulations of a Compression Corner Geometry Using Wall-Modeled LES Methods in Loci/CHEM

As computing technology continues to improve, simulating unsteady aerodynamic environments on launch vehicle geometries becomes more viable. For NASA’s Space Launch System, the flowfield is characterized by large regions of unsteady turbulent wall-bounded flow. Simulating these unsteady wall-bounded environments is of interest to the SLS Aerodynamics team. Wall-modeled LES methods are currently the best approach for simulating these environments in engineering applications. Less-expensive computationally than fully-resolved methods while maintaining many of the benefits in simulating unsteady environments. Before applying these methods blindly to large geometries, best practices can first be applied and understood on smaller canonical problems.

Bryson Frank↗

NASA NTRS1989

Numerical Simulation of Flow Through an Artificial Heart

A solution procedure was developed that solves the unsteady, incompressible Navier-Stokes equations, and was used to numerically simulate viscous incompressible flow through a model of the Pennsylvania State artificial heart. The solution algorithm is based on the artificial compressibility method, and uses flux-difference splitting to upwind the convective terms; a line-relaxation scheme is used to solve the equations. The time-accuracy of the method is obtained by iteratively solving the equations at each physical time step. The artificial heart geometry involves a piston-type action with a moving solid wall. A single H-grid is fit inside the heart chamber. The grid is continuously compressed and expanded with a constant number of grid points to accommodate the moving piston. The computational domain ends at the valve openings where nonreflective boundary conditions based on the method of characteristics are applied. Although a number of simplifing assumptions were made regarding the geometry, the computational results agreed reasonably well with an experimental picture. The computer time requirements for this flow simulation, however, are quite extensive. Computational study of this type of geometry would benefit greatly from improvements in computer hardware speed and algorithm efficiency enhancements.

Rogers, Stuart E.↗

DOE OSTI2021

Deep Learning Coordinate-Free Quantum Chemistry

Computing quantum chemical properties of small molecules and polymers can provide insights valuable to physicists, chemists and biologists when designing new materials, catalysts, biological probes and drugs. Deep learning can compute quantum chemical properties accurately in a fraction of the time required by commonly used methods such as density functional theory (DFT). However, many of these deep learning architectures require energy minimized molecular geometries as input, which is also computationally expensive, and decreasing the reproducibility and throughput of these methods. In this study, we demonstrate that accurate quantum chemical computations can be performed without optimized geometries by operating in the coordinate-free domain using deep learning on graph encodings. Furthermore, we also find that the choice of graph-encoding architecture substantially affects the performance of these methods. The Wave architecture outperforms graph convolution architectures, particularly on complex molecules. Furthermore, the structures of these graph encoding architectures provide an opportunity to probe an important, outstanding question in quantum mechanics: What types of quantum chemical properties can be represented by local-variable models? We find that Wave, a local-variable model, is more accurately calculates quantum chemical properties. Graph convolutional architectures require global variables, and are not as effective as as Wave. We anticipate that coordinate-free, deep-learning models of quantum chemistry will become valuable tools in chemistry and biology, enabling researchers to rapidly screen chemical databases or identify new molecules using automated, de-novo design algorithms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗