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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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DOE OSTI2016

SU-F-T-211: Evaluation of a Dual Focusing Magnet System for the Treatment of Small Proton Targets

Purpose: To investigate magnetic focusing for small volume proton targets using a doublet combination of quadrupole rare earth permanent magnet Halbach cylinder assemblies Methods: Monte Carlo computer simulations were performed using the Geant4 toolkit to compare dose depositions of proton beams transported through two focusing magnets or in their absence. Proton beams with energies of 127 MeV and initial diameters of 5, 8 and 10 mm were delivered through two identical focusing magnets similar to those currently in experimental use at Loma Linda University Medical Center. Analogous experiments used optimized configurations based on the simulation results. Dose was measured by a diode detector and Gafchromic EBT3 film and compared to simulation data. Based on results from the experimental data, an additional set of simulations was performed with an initial beam diameter of 18 mm and a two differing length magnets (40mm & 68mm). Results: Experimental data matched well with Monte Carlo simulations. However, under conditions necessary to produce circular beam spots at target depth, magnetically focused beams using two identical 40 mm length magnets did not meet all of our performance criteria of circular beam spots, improved peak to entrance (P/E) dose ratios and dose delivery efficiencies. The simulations using the longer 68 mm 2nd magnet yielded better results with 34% better P/E dose ratio and 20–50% better dose delivery efficiencies when compared to unfocused 10 mm beams. Conclusion: While magnetic focusing using two magnets with identical focusing power did not yield desired results, ongoing Monte Carlo simulations suggest that increasing the length of the 2nd magnet to 68 mm could improve P/E dose ratios and dose efficiencies. Future work includes additional experimental validation of the longer 2nd magnet setup as well as experiments with triplet magnet systems. This project was sponsored with funding from the Department of Defense (DOD# W81XWH-BAA-10-1).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-201-04: Can the Dynamic Library of Flap Applicators Replace Treatment Planning in Surface Brachytherapy?

Purpose: Contemporary brachytherapy treatment planning systems-(TPS) include the applicator model libraries to improve digitization; however, the library of surface-flap-applicators-(SFA) is not incorporated into the commercial TPS. We propose the dynamic library-(DL) for SFA and investigate if such library can eliminate applicator reconstruction, source activation and dose normalization. Methods: DL was generated for the SFA using the C++class libraries of the Visualization Toolkit-(VTK) and Qt-application framework for complete abstraction of the graphical interface. DL was designed such that the user can initially choose the size of the applicator that corresponds to the one clinically placed to the patient. The virtual applicator-(VA) has an elastic property so that it can be registered to the clinical CT images with a real applicator-(RA) on it. The VA and RA matching is performed by adjusting the position and curvature of the VA. The VA does not elongate or change its size so each catheter could always be at a distance of 5mm from the skin and 10mm apart from the closest catheter maintaining the physical accuracy of the clinical setup. Upon the applicator placement, the dwell positions were automatically activated, and the dose is normalized to the prescription depth. The accuracy of source positioning was evaluated using various applicator sizes. Results: The accuracy of the applicator placement was in the sub-millimeter range. The time-study reveals that up to 50% of the planning time can be saved depending on the complexity of the clinical setup. Unlike in the classic approach, the planning time was not highly dependent on the applicator size. Conclusion: The practical benefits of the DL of the SFA were demonstrated. The time demanding planning processes can be partially automated. Consequently, the planner can dedicate effort to fine tuning, which can result in the improvement of the quality of treatment plans in surface brachytherapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-JeP2-15: Proton Beam Behavior in the Presence of Realistic Magnet Fields

Purpose: To investigate the effects of magnetic fields on proton therapy beams for integration with MRI. Methods: 3D magnetic fields from an open-bore superconducting MRI model (previously developed by our group) and 3D magnetic fields from an in-house gradient coil design were applied to various mono energetic proton pencil beam (80MeV to 250MeV) simulations. In all simulations, the z-axis of the simulation geometry coincided with the direction of the B0 field and magnet isocentre. In each simulation, the initial beam trajectory was varied. The first set of simulations performed was based on analytic magnetic force equations (analytic simulations), which could be rapidly calculated yet were limited to propagating proton beams in vacuum. The second set is full Monte Carlo (MC) simulations, which used GEANT4 MC toolkit. Metrics such as the beam position and dose profiles were extracted. Comparisons between the cases with and without magnetic fields present were made. Results: The analytic simulations served as verification checks for the MC simulations when the same simulation geometries were used. The results of the analytic simulations agreed with the MC simulations performed in vacuum. The presence of the MRI’s static magnetic field causes proton pencil beams to follow a slight helical trajectory when there were some initial off-axis components. The 80MeV, 150MeV, and 250MeV proton beams rotated by 4.9o, 3.6o, and 2.8o, respectively, when they reached z=0cm. The deflections caused by gradient coils’ magnetic fields show spatially invariant patterns with a maximum range of 0.5mm at z=0cm. Conclusion: This investigation reveals that both the MRI’s B0 and gradient magnetic fields can cause small but observable deflections of proton beams at energies studied. The MRI’s static field caused a rotation of the beam while the gradient coils’ fields effects were spatially invariant. Dr. B Gino Fallone is a co-founder and CEO of MagnetTx Oncology Solutions (under discussions to license Alberta bi-planar linac MR for commercialization)

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-TeP4-13: Interfraction Treatment Monitoring Using Integrated Invivo EPID Images

Purpose: To investigate inter-fraction differences of dose delivery by analyzing portal images acquired during treatment and implement an automated system to generate a report for each fraction. Large differences in images between fractions can alert the physicist of possible machine performance issues or patient set-up errors. Methods: A Varian Novalis Tx equipped with a HD120 MLC and aS1000 electronic portal imaging device (EPID) was used in our study. EPID images are acquired in continuous acquisition mode for 32 volumetric arc therapy (VMAT) patients. The images are summed to create an image for each arc and a single image for each fraction. The first fraction is designated as the reference unless a machine error prevented acquisition of all images. The images for each beam as well as the fraction image are compared using gamma analysis at 1%/1mm, 2%/2mm and 3%/3mm. A report is then generated using an in house MatLab program containing the comparison for the current fraction as well as a history of previous fractions. The reports are automatically sent via email to the physicist for review. Fractions in which the total number of images was not within 5% of the reference number of images were not included in the results. Results: 91 of the 182 fractions recorded an image count within 5% of the reference. Gamma averages over all fractions and patients were 96.2% ±0.8% at 3%/3mm, 92.9% ±1% at 2%/2mm and 80.6% ±1.8% at 1%/1mm. The SD between fractions for each patient ranged from .004% to 10.4%. Of the 91 fractions 3 flagged due to low gamma values. After further investigation no significant errors were found. Conclusion: This toolkit can be used for in-vivo monitoring of treatment plan delivery an alert the physics staff of any inter-fraction discrepancies that may require further investigation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TU-H-CAMPUS-TeP3-03: Dose Enhancement by Gold Nanoparticles Around the Bragg Peak of Proton Beams

Purpose: To make clear the spatial distribution of dose enhancement around gold nanoparticles (GNPs) located near the proton Bragg peak, and to evaluate the potential of GNPs as a radio sensitizer. Methods: The dose enhancement by electrons emitted from GNPs under proton irradiation was estimated by Geant4 Monte Carlo simulation toolkit in two steps. In an initial macroscopic step, 100 and 195 MeV proton beams were incident on a water cube, 30 cm on a side. Energy distributions of protons were calculated at four depths, 50% and 75% proximal to the Bragg peak, 100% peak, and 75% distal to the peak (P50, P75, Peak, and D75, respectively). In a subsequent microscopic step, protons with the energy distribution calculated above were incident on a 20 nm diameter GNP in a nanometer-size water box and the spatial distribution of dose around the GNP was determined for each energy distribution. The dose enhancement factor (DEF) was also deduced. Results: The dose enhancement effect was spread to several tens of nanometers in the both depth and radial directions. The enhancement area increased in the order of P50, P75, Peak, and D75 for both cases with 100 and 195 MeV protons. In every position around the Bragg peak, the 100 MeV beam resulted in a higher dose enhancement than the 195 MeV beam. At P75, the average and maximum DEF were 3.9 and 17.0 for 100 MeV, and 3.5 and 16.2 for 195 MeV, respectively. These results indicate that lower energy protons caused higher dose enhancement in this incident proton energy range. Conclusion: The dose enhancement around GNPs spread as the position in the Bragg peak region becomes deeper and depends on proton energy. It is expected that GNPs can be used as a radio sensitizer with consideration of the location and proton beam energy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

WE-DE-207B-08: Towards Standardization of X-Ray Filters in Digital Mammography-Enabled Breast Tomosynthesis Systems

Purpose: In digital breast tomosynthesis (DBT) systems capable of digital mammography (DM), Al filters are used during DBT and K-edge filters during DM. The potential for standardizing the x-ray filters with Al, instead of K-edge filters, was investigated with intent to reduce exposure duration and to promote a simpler system design. Methods: Analytical computations of the half-value thickness (HVT) and the photon fluence per mAs (photons/mm2/mAs) for K-edge filters (50µm Rh; 50µm Ag) were compared with Al filters of varying thickness. Two strategies for matching the HVT from K-edge and Al filtered spectra were investigated: varying the kVp for fixed Al thickness, or varying the Al thickness at matched kVp. For both strategies, Al filters were an order of magnitude thicker than K-edge filters. Hence, Monte Carlo simulations were conducted with the GEANT4 toolkit to determine if the scatter-to-primary ratio (SPR) and the point spread function of scatter (scatter PSF) differed between Al and K-edge filters. Results: Results show the potential for replacing currently used Kedge filters with Al. For fixed Al thickness (700µm), ±1 kVp and +(1–3) kVp change, matched HVT of Rh and Ag filtered spectra. At matched kVp, Al thickness range (650,750)µm and (750,860)µm matched the HVT from Rh and Ag filtered spectra. Photon fluence/mAs with Al filters were 1.5–2.5 times higher, depending on kVp and Al thickness, compared to K-edge filters. Although Al thickness was an order higher than K-edge filters, neither the SPR nor the scatter PSF differed from K-edge filters. Conclusion: The use of Al filters for digital mammography is potentially feasible. The increased fluence/mAs with Al could decrease exposure duration for the combined DBT+DM exam and simplify system design. Effect of x-ray spectrum change due to Al filtration on radiation dose, signal, noise, contrast and related metrics are being investigated. Funding support: Supported in part by NIH R21CA176470 and R01CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH or NCI.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-CD-206-08: An Anthropopathic Deformable Phantom for Geometric and Dose Accumulation Accuracy Validation of Deformable Image Registration

Purpose: To design and construct a three-dimensional (3D) anthropopathic abdominal phantom for evaluating deformable image registration (DIR) accuracy on images and dose deformation in adaptive radiation therapy (ART). Method: Organ moulds, including liver, kidney, spleen, stomach, vertebra and two metastasis tumors, are 3D printed using the contours from an ovarian cancer patient. The organ moulds are molded with deformable gels that made of different mixtures of polyvinyl chloride (PVC) and the softener dioctyl terephthalate. Gels with different densities are obtained by a polynomial fitting curve which describes the relation between the CT number and PVC-softener blending ratio. The rigid vertebras are constructed by moulding with white cement. The final abdominal phantom is assembled by arranging all the fabricated organs inside a hollow dummy according to their anatomies and sealed with deformable gel with averaged CT number of muscle and fat. Geometric and dosimetric landmarks are embedded inside the phantom for spatial accuracy and dose accumulation accuracy studies. Three DIR algorithms available in the open source DIR toolkit-DIRART, including the Demons, the Horn-Schunck and Lucas-Kanade method and the Level-Set Motion method, are tested using the constructed phantom. Results: Viscoelastic behavior is observed in the constructed deformable gel, which serves as an ideal material for the deformable phantom. The constructed abdominal phantom consists of highly realistic anatomy and the fabricated organs inside have close CT number to its reference patient. DIR accuracy studies conducted on the constructed phantom using three DIR approaches indicate that geometric accuracy of a DIR algorithm has achieved does not guarantee accuracy in dose accumulation. Conclusions: We have designed and constructed an anthropopathic abdominal deformable phantom with satisfactory elastic property, realistic organ density and anatomy. This physical phantom is recyclable and can be used for routine validations of DIR geometric accuracy and dose accumulation accuracy in ART. This work is supported in part by grant from VARIAN MEDICAL SYSTEMS INC, the National Natural Science Foundation of China (no 81428019 and no 81301940), the Guangdong Natural Science Foundation (2015A030313302) and the 2015 Pearl River S&T Nova Program of Guangzhou (201506010096).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Mechanism and dynamics of fatty acid photodecarboxylase

Photoenzymes are rare biocatalysts driven by absorption of a photon at each catalytic cycle; they inspire development of artificial photoenzymes with valuable activities. Fatty acid photodecarboxylase (FAP) is a natural photoenzyme that has potential applications in the bio-based production of hydrocarbons, yet its mechanism is far from fully understood. RATIONALE To elucidate the mechanism of FAP, we studied the wild-type (WT) enzyme from Chlorella variabilis (CvFAP) and variants with altered active-site residues using a wealth of techniques, including static and time-resolved crystallography and spectroscopy, as well as biochemical and computational approaches. RESULTS A 1.8-Å-resolution CvFAP x-ray crystal structure revealed a dense hydrogen-bonding network positioning the fatty acid carboxyl group in the vicinity of the flavin adenine dinucleotide (FAD) cofactor. Structures solved from free electron laser and low-dose synchrotron x-ray crystal data further highlighted an unusual bent shape of the oxidized flavin chromophore, and showed that the bending angle (14°) did not change upon photon absorption (step 1) or throughout the photocycle. Calculations showed that bending substantially affected the energy levels of the flavin. Structural and spectroscopic analysis of WT and mutant proteins targeting two conserved active-site residues, R451 and C432, demonstrated that both residues were crucial for proper positioning of the substrate and water molecules and for oxidation of the fatty acid carboxylate by 1 FAD* (~300 ps in WT FAP) to form FAD ∙– (step 2). Time-resolved infrared spectroscopy demonstrated that decarboxylation occured quasi-instantaneously upon this forward electron transfer, consistent with barrierless bond cleavage predicted by quantum chemistry calculations and with snapshots obtained by time-resolved crystallography. Transient absorption spectroscopy in H 2 O and D 2 O buffers indicated that back electron transfer from FAD ∙– was coupled to and limited by transfer of an exchangeable proton or hydrogen atom (step 3). Unexpectedly, concomitant with FAD ∙– reoxidation (to a red-shifted form FAD RS ) in 100 ns, most of the CO 2 product was converted, most likely into bicarbonate (as inferred from FTIR spectra of the cryotrapped FAD RS intermediate). Calculations indicated that this catalytic transformation involved an active-site water molecule. Cryo-Fourier transform infrared spectroscopy studies suggested that bicarbonate formation (step 4) was preceded by deprotonation of an arginine residue (step 3). At room temperature, the remaining CO 2 left the protein in 1.5 μs (step 4'). The observation of residual electron density close to C432 in electron density maps derived from time-resolved and cryocrystallography data suggests that this residue may play a role in stabilizing CO 2 and/or bicarbonate. Three routes for alkane formation were identified by quantum chemistry calculations; the one shown in the figure is favored by the ensemble of experimental data. CONCLUSION Finally, we provide a detailed and comprehensive characterization of light-driven hydrocarbon formation by FAP, which uses a remarkably complex mechanism including unique catalytic steps. We anticipate that our results will help to expand the green chemistry toolkit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Pharmacological Profiling of a Brugia malayi Muscarinic Acetylcholine Receptor as a Putative Antiparasitic Target

The diversification of anthelmintic targets and mechanisms of action will help ensure the sustainable control of nematode infections in response to the growing threat of drug resistance. G protein-coupled receptors (GPCRs) are established drug targets in human medicine but remain unexploited as anthelmintic substrates despite their important roles in nematode neuromuscular and physiological processes. Bottlenecks in exploring the druggability of parasitic nematode GPCRs include a limited helminth genetic toolkit and difficulties establishing functional heterologous expression. In an effort to address some of these challenges, we profile the function and pharmacology of muscarinic acetylcholine receptors in the human parasite Brugia malayi, an etiological agent of human lymphatic filariasis. While acetylcholine-gated ion channels are intensely studied as targets of existing anthelmintics, comparatively little is known about metabotropic receptor contributions to parasite cholinergic signaling. Using multivariate phenotypic assays in microfilariae and adults, we show that nicotinic and muscarinic compounds disparately affect parasite fitness traits. We identify a putative G protein-linked acetylcholine receptor of B. malayi (Bma-GAR-3) that is highly expressed across intramammalian life stages and adapt spatial RNA in situ hybridization to map receptor transcripts to critical parasite tissues. Tissue-specific expression of Bma-gar-3 in Caenorhabditis elegans (body wall muscle, sensory neurons, and pharynx) enabled receptor deorphanization and pharmacological profiling in a nematode physiological context. Finally, we developed an image-based feeding assay as a reporter of pharyngeal activity to facilitate GPCR screening in parasitized strains. We expect that these receptor characterization approaches and improved knowledge of GARs as putative drug targets will further advance the study of GPCR biology across medically important nematodes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Tools for genetic engineering and gene expression control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides

ABSTRACT Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts that have the potential to contribute to the sustainable bioeconomy. Among the Alphaproteobacteria, Novosphingobium aromaticivorans , Rhodobacter sphaeroides , and Zymomonas mobilis show promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit for Z. mobilis , N. aromaticivorans and R. sphaeroides still need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools for N. aromaticivorans and R. sphaeroides to address these issues. We demonstrate that Tn 7 transposition is an effective approach for introducing engineered DNA into the chromosome of N. aromaticivorans and R. sphaeroides . We screen a synthetic promoter library to identify isopropyl β-D-1-thiogalactopyranoside-inducible promoters with regulated activity in both organisms (up to ~15-fold induction in N. aromaticivorans and ~5-fold induction in R. sphaeroides ). Combining Tn 7 integration with promoters from our library, we establish CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) interference systems for N. aromaticivorans and R. sphaeroides (up to ~10-fold knockdown in N. aromaticivorans and R. sphaeroides ) that can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these species and other Alphaproteobacteria. IMPORTANCE It is important to increase our understanding of the microbial world to improve health, agriculture, the environment, and biotechnology. For example, building a sustainable bioeconomy depends on the efficient conversion of plant material to valuable biofuels and bioproducts by microbes. One limitation in this conversion process is that microbes with otherwise promising properties for conversion are challenging to genetically engineer. Here we report genetic tools for Novosphingobium aromaticivorans and Rhodobacter sphaeroides that add to the burgeoning set of tools available for genome engineering and gene expression in Alphaproteobacteria. Our approaches allow straightforward insertion of engineered pathways into the N. aromaticivorans or R. sphaeroides genome and control of gene expression by inducing genes with synthetic promoters or repressing genes using CRISPR interference. These tools can be used in future work to gain additional insight into these and other Alphaproteobacteria and to aid in optimizing yield of biofuels and bioproducts.

Hall, Ashley N.↗
DOE OSTI2020

Development of Strong Anaerobic Fluorescent Reporters for Clostridium acetobutylicum and Clostridium ljungdahlii Using HaloTag and SNAP-tag Proteins

One of the biggest limitations in the study and engineering of anaerobic Clostridium organisms is the lack of strong fluorescent reporters capable of strong and real-time fluorescence. Recently, we developed a strong fluorescent reporter system for Clostridium organisms based on the FAST protein. Here, we report the development of two new strong fluorescent reporter systems for Clostridium organisms based on the HaloTag and SNAP-tag proteins, which produce strong fluorescent signals when covalently bound to fluorogenic ligands. These new fluorescent reporters are orthogonal to the FAST ligands and to each other, allowing for simultaneous labeling and visualization. We used HaloTag and SNAP-tag to label the strictly anaerobic organisms Clostridium acetobutylicum and Clostridium ljungdahlii. We have also identified a new strong promoter for protein expression in C. acetobutylicum, based on the phosphotransacetylase gene (pta) from C. ljungdahlii. Furthermore, the HaloTag and the SNAP-tag, in combination with the previously described FAST system, were successfully used to measure cell populations in bacterial mixed cultures and showed the simultaneous orthogonal labeling of HaloTag and SNAP-tag together with the FAST protein reporter. Finally, we show the expression of recombinant fusion protein of FAST and the ZapA division protein (from C. acetobutylicum) in C. ljungdahlii. The availability of multiple strong fluorescent reporters is a major addition to the genetic toolkit of Here, Clostridium and other anaerobes that will lead to better understanding of these unique organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

With its ability to catabolize a wide variety of carbon sources and a growing engineering toolkit, Pseudomonas putida KT2440 is emerging as an important chassis organism for metabolic engineering. Despite advances in our understanding of the organism, many gaps remain in our knowledge of the genetic basis of its metabolic capabilities. The gaps are particularly noticeable in our understanding of both fatty acid and alcohol catabolism, where many paralogs putatively coding for similar enzymes coexist, making biochemical assignment via sequence homology difficult. To rapidly assign function to the enzymes responsible for these metabolisms, we leveraged random barcode transposon sequencing (RB-Tn-Seq). Global fitness analyses of transposon libraries grown on 13 fatty acids and 10 alcohols produced strong phenotypes for hundreds of genes. Fitness data from mutant pools grown on fatty acids of varying chain lengths indicated specific enzyme substrate preferences and enabled us to hypothesize that DUF1302/DUF1329 family proteins potentially function as esterases. From the data, we also postulate catabolic routes for the two biogasoline molecules isoprenol and isopentanol, which are catabolized via leucine metabolism after initial oxidation and activation with coenzyme A (CoA). Because fatty acids and alcohols may serve as both feedstocks and final products of metabolic-engineering efforts, the fitness data presented here will help guide future genomic modifications toward higher titers, rates, and yields. IMPORTANCE To engineer novel metabolic pathways into P. putida , a comprehensive understanding of the genetic basis of its versatile metabolism is essential. Here, we provide functional evidence for the putative roles of hundreds of genes involved in the fatty acid and alcohol metabolism of the bacterium. These data provide a framework facilitating precise genetic changes to prevent product degradation and to channel the flux of specific pathway intermediates as desired.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice

This study explores viral community structure and function in remote and extreme Arctic environments, including subzero brines within marine layers of permafrost and sea ice, using a modern viral ecogenomics toolkit for the first time. In addition to providing foundational data sets for these climate-threatened habitats, we found evidence that the viruses had habitat specificity, infected dominant microbial hosts, encoded host-derived metabolic genes, and mediated horizontal gene transfer among hosts. These results advance our understanding of the virosphere and how viruses influence extreme ecosystems. More broadly, the evidence that virally mediated gene transfers may be limited by host range in these extreme habitats contributes to a mechanistic understanding of genetic exchange among microbes under stressful conditions in other systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

TQ-bifurcations in discrete dynamical systems: Analysis of qualitative rearrangements of the oscillation mode

A new class of bifurcations is defined in discrete dynamical systems, and methods for their diagnostics and the analysis of their properties are presented. The TQ-bifurcations considered are implemented in discrete mappings and are related to the qualitative rearrangement of the shape of trajectories in an extended space of states. Within the demonstration of the main capabilities of the toolkit, an analysis is carried out of a logistic mapping in a domain to the right of the period-doubling limit point. Five critical values of the parameter are found for which the geometric structure of the trajectories of the mapping experiences a qualitative rearrangement. In addition, an analysis is carried out of the so-called “trace map,” which arises in the problems of quantum-mechanical description of various properties of discrete crystalline and quasicrystalline lattices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Chemical Composition Analysis for X-Ray Transport Container Scans

It is important for national security to control the movement of dangerous or strategically cargo such as explosives, radioactive materials, rare and precious metals. This control can be provided by scanning transport containers by gamma rays. In this report the existing technique for scanning (dual energy method) is considered and the alternative method based on measuring the energy distribution of gamma rays is proposed. For estimation perspectives of the proposing method, the corresponding simulation was conducted by using the GEANT4 toolkit. The example of the algorithm of reconstruction the chemical composition of the scanned object is also considered. In addition the experiment for estimation energy resolution of the detector based on a scintillation crystal BGO and SiPM was carried out.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Background model for the NaI(Tl) crystals in COSINE-100

The COSINE-100 dark matter search experiment is an array of NaI(Tl) crystal detectors located in the Yangyang Underground Laboratory (Y2L). To understand measured backgrounds in the NaI(Tl) crystals we have performed Monte Carlo simulations using the Geant4 toolkit and developed background models for each crystal that consider contributions from both internal and external sources, including cosmogenic nuclides. The background models are based on comparisons of measurement data with Monte Carlo simulations that are guided by a campaign of material assays and are used to evaluate backgrounds and identify their sources. The average background level for the six crystals (70 kg total mass) that are studied is 3.5 counts/day/keV/kg in the (2–6) keV energy interval. The dominant contributors in this energy region are found to be 210 Pb and 3 H.

36 MATERIALS SCIENCE↗
DOE OSTI2015

ParaView Catalyst: Enabling In Situ Data Analysis and Visualization

Computer simulations are growing in sophistication and producing results of ever greater fidelity. This trend has been enabled by advances in numerical methods and increasing computing power. However these advances come with several costs including massive increases in data size, difficulties examining output data, challenges in configuring simulation runs, and difficulty debugging running codes. Interactive visualization tools, like ParaView, have been used for post-processing of simulation results. However, the increasing data sizes, and limited storage and bandwidth make high fidelity post-processing impractical. In situ analysis is recognized as one of the ways to address these challenges. In situ analysis moves some of the post-processing tasks in line with the simulation code thus short circuiting the need to communicate the data between the simulation and analysis via storage. ParaView Catalyst is a data processing and visualization library that enables in situ analysis and visualization. Built on and designed to interoperate with the standard visualization toolkit VTK and the ParaView application, Catalyst enables simulations to intelligently perform analysis, generate relevant output data, and visualize results concurrent with a running simulation. Here, we provide an overview of the Catalyst framework and some of the success stories.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

What does fault tolerant Deep Learning need from MPI?

Deep Learning (DL) algorithms have become the {\em de facto} Machine Learning (ML) algorithm for large scale data analysis. DL algorithms are computationally expensive -- even distributed DL implementations which use MPI require days of training (model learning) time on commonly studied datasets. Long running DL applications become susceptible to faults -- requiring development of a fault tolerant system infrastructure, in addition to fault tolerant DL algorithms. This raises an important question: {\em What is needed from MPI for designing fault tolerant DL implementations?} In this paper, we address this problem for permanent faults. We motivate the need for a fault tolerant MPI specification by an in-depth consideration of recent innovations in DL algorithms and their properties, which drive the need for specific fault tolerance features. We present an in-depth discussion on the suitability of different parallelism types (model, data and hybrid); a need (or lack thereof) for check-pointing of any critical data structures; and most importantly, consideration for several fault tolerance proposals (user-level fault mitigation (ULFM), Reinit) in MPI and their applicability to fault tolerant DL implementations. We leverage a distributed memory implementation of Caffe, currently available under the Machine Learning Toolkit for Extreme Scale (MaTEx). We implement our approaches by extending MaTEx-Caffe for using ULFM-based implementation. Our evaluation using the ImageNet dataset and AlexNet neural network topology demonstrates the effectiveness of the proposed fault tolerant DL implementation using OpenMPI based ULFM.

Amatya, Vinay C.↗