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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 OSTI2015

Designer diatom episomes delivered by bacterial conjugation

Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify a yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Proton radiation effects in indium oxide using cascade molecular dynamics simulations

Metal oxide (MO) semiconductors, characterized by their wide band gaps and notable charge transport properties, are promising candidates for electronic applications in extreme environments, including near-Earth space. However, atomistic simulations of radiation–matter interactions in MOs remain challenging due to the limitations of existing interatomic potentials, which often fail to capture both the short-range repulsive forces essential for radiation damage modeling and the long-range electrostatic effects governing defect evolution. In this work, we develop a customized interatomic potential tailored for radiation damage simulations in indium oxide (In 2 O 3 ) as a model system, a representative MO material. Our potential integrates the Ziegler-Biersack-Littmark potential to accurately describe short-range interactions with Buckingham and Coulombic potentials to account for long-range forces. We perform molecular dynamics simulations of low-energy proton irradiation using this custom potential. We employ the primary knock-on atom (PKA) cascade method to study atomic displacements and primary defect formation. Simulations were conducted for 1 keV proton irradiation in four randomly chosen directions, and PKA-driven defect analyses at 5, 10, and 15 keV to examine the effects of direction and energy level on damage generation. Our results provide insight into the impact of irradiation direction and energy level on the cascade evolution and defect formation mechanisms.

Atomistic simulations↗
DOE OSTI2015

NONLINEAR EFFECTS IN PARTICLE TRANSPORT IN STOCHASTIC MAGNETIC FIELDS

Collisional particle transport in stochastic magnetic fields is studied using a semi-analytical method. The aim is to determine the influence of the nonlinear effects that occur in the magnetic field line random walk on particle transport. We show that particle transport coefficients can be strongly influenced by the magnetic line trapping. The conditions that correspond to these nonlinear regimes are determined. We also analyze the effects produced by the space variation of the large-scale magnetic field. We show that an average drift is generated by the gradient of the magnetic field, which strongly increases and reverses its orientation in the nonlinear regime.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Quantum mixed state compiling

The task of learning a quantum circuit to prepare a given mixed state is a fundamental quantum subroutine. We present a variational quantum algorithm (VQA) to learn mixed states which is suitable for near-term hardware. Our algorithm represents a generalization of previous VQAs that aimed at learning preparation circuits for pure states. We consider two different ansätze for compiling the target state; the first is based on learning a purification of the state and the second on representing it as a convex combination of pure states. In both cases, the resources required to store and manipulate the compiled state grow with the rank of the approximation. Thus, by learning a lower rank approximation of the target state, our algorithm provides a means of compressing a state for more efficient processing. As a byproduct of our algorithm, one effectively learns the principal components of the target state, and hence our algorithm further provides a new method for principal component analysis. We investigate the efficacy of our algorithm through extensive numerical implementations, showing that typical random states and thermal states of many body systems may be learnt this way. Additionally, we demonstrate on quantum hardware how our algorithm can be used to study hardware noise-induced states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Impact of Alloy-Disorder-Induced Localization on Hole Diffusion in Highly Excited c -Plane and m -Plane (In, Ga) N Quantum Wells

The diffusion coefficient of holes can provide knowledge about carrier localization in (In, Ga)N, where the carrier dynamics are altered by randomly fluctuating potential landscape. In group-III nitrides, the diffusivity of holes is difficult to measure by electrical methods but it can be studied using optical techniques. Here, we investigate the dependence of the hole diffusion coefficient on direction and carrier density in c-plane and m-plane (In, Ga)N structures by employing the light-induced transient-grating technique. We show that the hole diffusion coefficient is anisotropic in the m-plane structure, where it is several times larger along the a crystallographic direction than along the c direction. Such anisotropy is observed within the broad range of carrier densities from 10 18 to 10 20 cm –3 . The diffusivity changes nonmonotonously with increasing photoexcitation, this dependence being different in thick and thin layers. We argue that an unexpectedly high diffusion coefficient at low carrier densities in thick quantum wells can be a signature of efficient hole transport via percolative paths occurring due to compositional disorder. In turn, a decrease of diffusivity with the excitation can reflect the effect of Coulomb blockade of these paths. Lastly, we demonstrate that disorder impacts carrier diffusivity even at carrier densities above 10 19 cm –3 , where the overflow of localized states must be included to explain the observed increase of the diffusion coefficient with the carrier density.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Prediction of novel high-pressure H 2 O -NaCl and carbon oxide compounds with a symmetry-driven structure search algorithm

Crystal structure prediction with theoretical methods is particularly challenging when unit cells with many atoms need to be considered. Here we employ a symmetry-driven structure search (SYDSS) method and combine it with density functional theory (DFT) to predict novel crystal structures at high pressure. We sample randomly from all 1,506 Wyckoff positions of the 230 space groups to generate a set of initial structures. During the subsequent structural relaxation with DFT, existing symmetries are preserved, but the symmetries and the space group may change as atoms move to more symmetric positions. By construction, our algorithm generates symmetric structures with high probability without excluding any configurations. This improves the search efficiency, especially for large cells with 20 atoms or more. We apply our SYDSS algorithm to identify stoichiometric (H 2 O) n -(NaCl) m and C n O m compounds at high pressure. We predict a novel H 2 O-NaCl structure with Pnma symmetry to form at 3.4 Mbar, which is within the range of diamond anvil experiments. In addition, we predict a novel C 2 O structure at 19.8 Mbar and C4O structure at 44.0 Mbar with Pbca and C2/m symmetry respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Finding Matrix Product State Representations of Highly Excited Eigenstates of Many-Body Localized Hamiltonians

A key property of many-body localized Hamiltonians is the area law entanglement of even highly excited eigenstates. Matrix product states (MPS) can be used to efficiently represent low entanglement (area law) wave functions in one dimension. An important application of MPS is the widely used density matrix renormalization group (DMRG) algorithm for finding ground states of one-dimensional Hamiltonians. Here, we develop two algorithms, the shift-and-invert MPS (SIMPS) and excited state DMRG which find highly excited eigenstates of many-body localized Hamiltonians. Excited state DMRG uses a modified sweeping procedure to identify eigenstates, whereas SIMPS applies the inverse of the shifted Hamiltonian to a MPS multiple times to project out the targeted eigenstate. To demonstrate the power of these methods, we verify the breakdown of the eigenstate thermalization hypothesis in the many-body localized phase of the random field Heisenberg model, show the saturation of entanglement in the many-body localized phase, and generate local excitations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

SU-E-T-14: A Feasibility Study of Using Modified AP Proton Beam for Post-Operative Pancreatic Cancer Therapy

Purpose: Due to the unpredictability of bowel gas movement, the PA beam direction is always favored for robust proton therapy in post-operative pancreatic cancer treatment. We investigate the feasibility of replacing PA beam with a modified AP beam to take the bowel gas uncertainty into account. Methods: Nine post-operative pancreatic cancer patients treated with proton therapy (5040cGy, 28 fractions) in our institution were randomly selected. The original plan uses PA and lateral direction passive-scattering proton beams. Beam weighting is about 1:1. All patients received weekly verification CTs to assess the daily variations(total 17 verification CTs). The PA direction beam was replaced by two other groups of AP direction beam. Group AP: takes 3.5% range uncertainty into account. Group APmod: compensates the bowel gas uncertainty by expanding the proximal margin to 2cm more. The 2cm margin was acquired from the average bowel diameter in from 100 adult abdominal CT scans near pancreatic region (+/- 5cm superiorly and inferiorly). Dose Volume Histograms(DVHs) of the verification CTs were acquired for robustness study. Results: Without the lateral beam, Group APmod is as robust as Group PA. In Group AP, more than 10% of iCTV D98/D95 were reduced by 4–8%. LT kidney and Liver dose robustness are not affected by the AP/PA beam direction. There is 10% of chance that RT kidney and cord will be hit by AP proton beam due to the bowel gas. Compared to Group PA, APmod plan reduced the dose to kidneys and cord max significantly, while there is no statistical significant increase in bowel mean dose. Conclusion: APmod proton beam for the target coverage could be as robust as the PA direction without sacrificing too much of bowel dose. When the AP direction beam has to be selected, a 2cm proximal margin should be considered.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-578: On Definition of Minimum and Maximum Dose for Target Volume

Purpose: This study aims to investigate the impact of different minimum and maximum dose definitions in radiotherapy treatment plan quality evaluation criteria by using tumor control probability (TCP) models. Methods: Dosimetric criteria used in RTOG 1308 protocol are used in the investigation. RTOG 1308 is a phase III randomized trial comparing overall survival after photon versus proton chemoradiotherapy for inoperable stage II-IIIB NSCLC. The prescription dose for planning target volume (PTV) is 70Gy. Maximum dose (Dmax) should not exceed 84Gy and minimum dose (Dmin) should not go below 59.5Gy in order for the plan to be “per protocol” (satisfactory).A mathematical model that simulates the characteristics of PTV dose volume histogram (DVH) curve with normalized volume is built. The Dmax and Dmin are noted as percentage volumes Dη% and D(100-δ)%, with η and d ranging from 0 to 3.5. The model includes three straight line sections and goes through four points: D95%= 70Gy, Dη%= 84Gy, D(100-δ)%= 59.5 Gy, and D100%= 0Gy. For each set of η and δ, the TCP value is calculated using the inhomogeneously irradiated tumor logistic model with D50= 74.5Gy and γ50=3.52. Results: TCP varies within 0.9% with η; and δ values between 0 and 1. With η and η varies between 0 and 2, TCP change was up to 2.4%. With η and δ variations from 0 to 3.5, maximum of 8.3% TCP difference is seen. Conclusion: When defined maximum and minimum volume varied more than 2%, significant TCP variations were seen. It is recommended less than 2% volume used in definition of Dmax or Dmin for target dosimetric evaluation criteria. This project was supported by NIH grants U10CA180868, U10CA180822, U24CA180803, U24CA12014 and PA CURE Grant.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2015

SU-E-T-647: Quality Assurance of VMAT by Gamma Analysis Dependence On Low-Dose Threshold

Purpose: The AAPM TG-119 instructed institutions to use low-dose threshold (LDT) of 10% or a ROI determined by the jaw when they collected gamma analysis QA data of planar dose distribution. Also, based on a survey by Nelms and Simon, more than 70% of institutions use a LDT between 0% and 10% for gamma analysis. However, there are no clinical data to quantitatively demonstrate the impact of the LDT on the gamma index. Therefore, we performed a gamma analysis with LDTs of 0% to 15% according to both global and local normalization and different acceptance criteria: 3%/3 mm, 2%/2 mm, and 1%/1 mm. Methods: A total of 30 treatment plans—10 head and neck, 10 brain, and 10 prostate cancer cases—were randomly selected from the Varian Eclipse TPS, retrospectively. For the gamma analysis, a predicted portal image was acquired through a portal dose calculation algorithm in the Eclipse TPS, and a measured portal image was obtained using a Varian Clinac iX and an EPID. Then, the gamma analysis was performed using the Portal Dosimetry software. Results: For the global normalization, the gamma passing rate (%GP) decreased as the LDT increased, and all cases of low-dose thresholds exhibited a %GP above 95% for both the 3%/3 mm and 2%/2 mm criteria. However, for local normalization, the %GP increased as LDT increased. The gamma passing rate with LDT of 10% increased by 6.86%, 9.22% and 6.14% compared with the 0% in the case of the head and neck, brain and prostate for 3%/3 mm criteria, respectively. Conclusion: Applying the LDT in the global normalization does not have critical impact to judge patient-specific QA results. However, LDT for the local normalization should be carefully selected because applying the LDT could affect the average of the %GP to increase rapidly.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2015

A Representative Democracy to Reduce Interdependency in a Multimodel Ensemble

The collection of Earth system models available in the archive of phase 5 of CMIP (CMIP5) represents, at least to some degree, a sample of uncertainty of future climate evolution. The presence of duplicated code as well as shared forcing and validation data in the multiple models in the archive raises at least three potential problems: biases in the mean and variance, the overestimation of sample size, and the potential for spurious correlations to emerge in the archive because of model replication. Analytical evidence is presented to demonstrate that the distribution of models in the CMIP5 archive is not consistent with a random sample, and a weighting scheme is proposed to reduce some aspects of model codependency in the ensemble. A method is proposed for selecting diverse and skillful subsets of models in the archive, which could be used for impact studies in cases where physically consistent joint projections of multiple variables (and their temporal and spatial characteristics) are required.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Quantifying Leaf Chlorophyll Concentration of Sorghum from Hyperspectral Data Using Derivative Calculus and Machine Learning

Leaf chlorophyll concentration (LCC) is an important indicator of plant health, vigor, physiological status, productivity, and nutrient deficiencies. Hyperspectral spectroscopy at leaf level has been widely used to estimate LCC accurately and non-destructively. This study utilized leaf-level hyperspectral data with derivative calculus and machine learning to estimate LCC of sorghum. We calculated fractional derivative (FD) orders starting from 0.2 to 2.0 with 0.2 order increments. Additionally, 43 common vegetation indices (VIs) were calculated from leaf spectral reflectance factor to make comparisons with reflectance-based data. Within the modeling pipeline, three feature selection methods were assessed: Pearson’s correlation coefficient (PCC), partial least squares based variable importance in the projection (VIP), and random forest-based mean decrease impurity (MDI). Finally, we used partial least squares regression (PLSR), random forest regression (RFR), support vector regression (SVR), and extreme learning regression (ELR) to estimate the LCC of sorghum. Results showed that: (1) increasing derivative order can show improved model performance until certain order for reflectance-based analysis; however, it is inconclusive to state that a particular order is optimal for estimating LCC of sorghum; (2) VI-based modeling outperformed derivative augmented reflectance factor-based modeling; (3) mean decrease impurity was found effective in selecting sensitive features from large feature space (reflectance-based analysis), whereas simple Pearson’s correlation coefficient worked better with smaller feature space (VI-based analysis); and (4) SVR outperformed all other models within reflectance-based analysis; alternatively, ELR with VIs from original reflectance yielded slightly better results compared to all other models.

47 OTHER INSTRUMENTATION↗
DOE OSTI2017

The Radiation Unit is Difficult for the General Public to Understand - An Easier Alternative Unit is Required - 17223

One of the difficult things to explain about nuclear power and/or radiation to the public is the 'radiation unit'. Especially after the Fukushima accident, many people are concerned about radiation, but over 70% of public who responded to the survey do not understand what the Bq (Becquerel) refers to. Changing the SI unit (International System of Units) is not easy, and instead, auxiliary units can be used. We considered several auxiliary units: one using an index number (like that for earthquakes), one that makes a comparison to general drug risk, one that makes a comparison to an amount of foodstuff (like BED), an introducing index comparing annual dose limit, using number compared to the background, and colorizing (i.e, red, green, blue). KHNP-CRI surveyed the public about radiation and radiation unit indexes to determine which was easiest to understand. For the question 'Do you know what the radiation unit Becquerel (Bq) is?', over 70% answered 'No'. When asked,'Do you think radioactivity is contagious and can be transmitted through a person's respiratory system or via skin contact?', over 47% answered 'It is definitely or possibly contagious'. When asked, 'Which would you prefer as an easier to understand radiation auxiliary unit, if it were to be changed?', over 70% preferred 'colorizing or figure'. It is interesting that men prefer figures whereas women prefer colorizing. The sample population of the survey was 500 adult men and women in Korea. The sampling error was based on random sampling, a confidence interval of 95%, and a standard maximum allowable sampling error of ± 4.4% point. The survey method was 'Computer Aided Telephone Interview' (CATI). (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2014

Alignment of gold nanorods by angular photothermal depletion

In this paper, we demonstrate that a high degree of alignment can be imposed upon randomly oriented gold nanorod films by angular photothermal depletion with linearly polarized laser irradiation. The photothermal reshaping of gold nanorods is observed to follow quadratic melting model rather than the threshold melting model, which distorts the angular and spectral hole created on 2D distribution map of nanorods to be an open crater shape. We have accounted these observations to the alignment procedures and demonstrated good agreement between experiment and simulations. The use of multiple laser depletion wavelengths allowed alignment criteria over a large range of aspect ratios, achieving 80% of the rods in the target angular range. We extend the technique to demonstrate post-alignment in a multilayer of randomly oriented gold nanorod films, with arbitrary control of alignment shown across the layers. Photothermal angular depletion alignment of gold nanorods is a simple, promising post-alignment method for creating future 3D or multilayer plasmonic nanorod based devices and structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Clinically applicable 53-Gene prognostic assay predicts chemotherapy benefit in gastric cancer: A multicenter study

BACKGROUND:We previously established a 53-gene prognostic signature for overall survival (OS) of gastric cancer patients. This retrospective multi-center study aimed to develop a clinically applicable gene expression detection assay and to investigate the prognostic value of this signature. METHODS:A TCGA gastric adenocarcinoma cohort (TCGA-STAD) was used for comparing 53-gene signature with other gene signatures. A high-throughput mRNA hybridization gene expression assay was developed to quantify the expression of 53-genes in formalin-fixed paraffin-embedded tissues of 540 patients enrolled from three hospitals. 180 patents were randomly selected from two hospitals to build a prognostic prediction model based on the 53-gene signature using leave-p-out (one-third out) cross-validation method together with Cox regression and Kaplan-Meier analysis, and the model was assessed on three validation cohorts. FINDINGS:In the evaluation phase, studies based on TCGA-STAD showed that the 53-gene signature was significantly superior to other three prognostic signatures and was independent of TCGA molecular subtypes and clinical factors. For clinical validation and utility, the prognostic scores were generated using the newly developed assay, which was reliable and sensitive, in 100 sampling training sets and were significantly associated with OS in 100 sampling validation sets. The scores were significantly associated with OS in three independent and combined validation cohorts, and in patients with stages II and III/IV. The multivariate Cox regression demonstrated that the prognostic power of the score was independent of clinical factors, consistent with those findings in the TCGA dataset. Finally, patients with good prognostic scores exhibited significantly a better 5-year OS rate from adjuvant FOLFOX chemotherapy after surgery than from other chemotherapies. INTERPRETATION:The 53-gene prognostic score system is clinically applicable for predicting the OS of patients independent of clinical factors in gastric cancers, which could also be a promising predictive biomarker for FOLFOX regimen. FUNDING:Chinese National Science and Technology, National Natural Science Foundation and Natural Science Foundation of Jiangsu Province.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

SU-E-QI-03: Compartment Modeling of Dynamic Brain PET - The Effect of Scatter and Random Corrections On Parameter Errors

Purpose: To investigate the effects of corrections for random and scattered coincidences on kinetic parameters in brain tumors, by using ten Monte Carlo (MC) simulated dynamic FLT-PET brain scans. Methods: The GATE MC software was used to simulate ten repetitions of a 1 hour dynamic FLT-PET scan of a voxelized head phantom. The phantom comprised six normal head tissues, plus inserted regions for blood and tumor tissue. Different time-activity-curves (TACs) for all eight tissue types were used in the simulation and were generated in Matlab using a 2-tissue model with preset parameter values (K1,k2,k3,k4,Va,Ki). The PET data was reconstructed into 28 frames by both ordered-subset expectation maximization (OSEM) and 3D filtered back-projection (3DFBP). Five image sets were reconstructed, all with normalization and different additional corrections C (A=attenuation, R=random, S=scatter): Trues (AC), trues+randoms (ARC), trues+scatters (ASC), total counts (ARSC) and total counts (AC). Corrections for randoms and scatters were based on real random and scatter sinograms that were back-projected, blurred and then forward projected and scaled to match the real counts. Weighted non-linearleast- squares fitting of TACs from the blood and tumor regions was used to obtain parameter estimates. Results: The bias was not significantly different for trues (AC), trues+randoms (ARC), trues+scatters (ASC) and total counts (ARSC) for either 3DFBP or OSEM (p<0.05). Total counts with only AC stood out however, with an up to 160% larger bias. In general, there was no difference in bias found between 3DFBP and OSEM, except in parameter Va and Ki. Conclusion: According to our results, the methodology of correcting the PET data for randoms and scatters performed well for the dynamic images where frames have much lower counts compared to static images. Generally, no bias was introduced by the corrections and their importance was emphasized since omitting them increased bias extensively.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Controlled Nonlinear Stochastic Delay Equations: Part II: Approximations and Pipe-Flow Representations

This is the second part of a work dealing with key issues that have not been addressed in the modeling and numerical optimization of nonlinear stochastic delay systems. We consider new classes of models, such as those with nonlinear functions of several controls (such as products), each with is own delay, controlled random Poisson measure driving terms, admissions control with delayed retrials, and others. Part I was concerned with issues concerning the class of admissible controls and their approximations, since the classical definitions are inadequate for our models. This part is concerned with transportation equation representations and their approximations. Such representations of nonlinear stochastic delay models have been crucial in the development of numerical algorithms with much reduced memory and computational requirements. The representations for the new models are not obvious and are developed. They also provide a template for the adaptation of the Markov chain approximation numerical methods.

97 MATHEMATICS AND COMPUTING↗