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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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At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

GANISP (GAN-assisted Importance SPlitting)

Genealogical importance splitting marches towards a rare event by iteratively selecting and replicating realizations that are headed towards a rare event. The replication step is made difficult when applied to deterministic systems as the initial conditions of the offspring realizations need to be adjusted. Typically, a random perturbation is applied to the offspring. For some cases, this cloning technique may not be adequate and prevent variance reduction in the probability estimate. A GAN-based replication process is proposed to address this limitation. The perturbations applied to the clones are physically consistent instead of being randomly chosen. The proposed method allows reducing the variance in the probability estimation.

Hassanaly, Malik↗
DOE OSTI2011

Vitreal Ocygenation in Retinal Ischemia Reperfusion

PURPOSE. To study the feasibility of anterior vitreal oxygenation for the treatment of acute retinal ischemia. METHODS. Twenty rabbits were randomized into an oxygenation group, a sham treatment group, and a no treatment group. Baseline electroretinography (ERG) and preretinal oxygen (PO2) measurements were obtained 3 to 5 days before surgery. Intraocular pressure was raised to 100 mm Hg for 90 minutes and then normalized. The oxygenation group underwent vitreal oxygenation for 30 minutes using intravitreal electrodes. The sham treatment group received inactive electrodes for 30 minutes while there was no intervention for the no treatment group. Preretinal PO2 in the posterior vitreous was measured 30 minutes after intervention or 30 minutes after reperfusion (no treatment group) and on postoperative days (d) 3, 6, 9, and 12. On d14, rabbits underwent ERG and were euthanatized.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions

Abstract Plants exhibit extensive environment-dependent intraspecific metabolic variation, which likely plays a role in determining variation in whole plant phenotypes. However, much of the work seeking to use natural variation to link genes and transcript’s impacts on plant metabolism has employed data from controlled environments. Here, we generated and analyzed data on the variation in the abundance of 26 metabolites across 660 maize inbred lines under field conditions. We employ these data and previously published transcript and whole plant phenotype data reported for the same field experiment to identify both genomic intervals (through genome-wide association studies (GWAS)) and transcripts (using both transcriptome-wide association studies (TWAS) and an explainable artificial intelligence (AI) approach based on random forest (RF)) associated with variation in metabolite abundance. Both genome-wide association and random forest-based methods identified substantial numbers of significant associations including genes with plausible links to the metabolites they are associated with. In contrast, the transcriptome-wide association identified only six significant associations. In three cases, genetic markers associated with metabolic variation in our study colocalized with markers linked to variation in non-metabolic traits scored in the same experiment. We speculate that the poor performance of transcriptome-wide association studies in identifying transcript-metabolite associations may reflect a high prevalence of non-linear interactions between transcripts and metabolites and/or a bias towards rare transcripts playing a large role in determining intraspecific metabolic variation.

Mathivanan, Ramesh Kanna↗
DOE OSTI2021

A Comparison of Time Series Gap-Filling Methods to Impute Solar Radiation Data

Complete solar resource datasets play a critical role at every stage of solar project phases. However, measured or modeled solar resource data come with significant uncertainties and usually suffer from several issues, including but not limited to, data gaps, data quality issue, etc. In order to mitigate these issues an appropriate data imputation method should be implemented to build a complete and reliable temporal (and spatial) database. Being motivated by this, in this study we compare the performances of eight different gap filling methods extensively by creating random and artificial data gaps in (i) hourly irradiance data for one year using a few locations of the National Solar Radiation Database (NSRDB) and (ii) one-minute ground measurement dataset from Surface Radiation Budget Network (SURFRAD) stations.

clearness index↗
DOE OSTI2025

Developing ML/AI Methods for High-Throughput Characterization of Multiple-Sensor Streams of Tokamak Dynamics for High-Speed Control (Final Report)

This project evaluated and developed new mathematical and algorithmic techniques capable of handling (in real-time) the growing amounts of data generated by modern fusion research. While existing numerical linear algebra (NLA) methods provide the backbone to classical data analysis and algorithms, these methods fundamentally do not port to distributed architectures nor do they allow low-latency data reduction for control. Motivated by the needs for modern fusion reactors, this project explored and implemented new numerical methods to characterize plasma dynamics, respond in real-time to discharge evolution, and to process massive-scale data accurately and rapidly more fully. This project links expertise in multiple-sensor diagnostics of tokamak plasma dynamics from Columbia University’s Plasma Physics Laboratory with expertise in massive-scale data reduction and extreme data control algorithms at Columbia University’s Data Science Institute. This interdisciplinary project (i) applied machine learning methods, (ii) implemented a properly-trained neural-network for very fast processing of high-speed plasma videography, and (ii) developed the applied mathematical methods, based on randomized-NLA (rNLA) routines, for data analysis, reduction, and real-time control. The Columbia University High Beta Tokamak-Extended Pulse (HBT-EP) facility provided data to test new algorithms and partnership with Columbia University's Data Sciences Institute evaluated the broader use of new algorithms for many challenging control applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Targeted mutagenesis and high-throughput screening of diversified gene and promoter libraries for isolating gain-of-function mutations

Targeted mutagenesis of a promoter or gene is essential for attaining new functions in microbial and protein engineering efforts. In the burgeoning field of synthetic biology, heterologous genes are expressed in new host organisms. Similarly, natural or designed proteins are mutagenized at targeted positions and screened for gain-of-function mutations. Here, we describe methods to attain complete randomization or controlled mutations in promoters or genes. Combinatorial libraries of one hundred thousands to tens of millions of variants can be created using commercially synthesized oligonucleotides, simply by performing two rounds of polymerase chain reactions. With a suitably engineered reporter in a whole cell, these libraries can be screened rapidly by performing fluorescence-activated cell sorting (FACS). Within a few rounds of positive and negative sorting based on the response from the reporter, the library can rapidly converge to a few optimal or extremely rare variants with desired phenotypes. Library construction, transformation and sequence verification takes 6–9 days and requires only basic molecular biology lab experience. Screening the library by FACS takes 3–5 days and requires training for the specific cytometer used. Further steps after sorting, including colony picking, sequencing, verification, and characterization of individual clones may take longer, depending on number of clones and required experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The PENELOPE Physics Models and Transport Mechanics. Implementation into Geant4

A translation of the PENELOPE physics subroutines to C++, designed as an extension of the GEANT4 toolkit, is presented. The Fortran code system PENELOPE performs Monte Carlo simulation of coupled electron-photon transport in arbitrary materials for a wide energy range, nominally from 50 eV up to 1 GeV. PENELOPE implements the most reliable interaction models that are currently available, limited only by the required generality of the code. In addition, the transport of electrons and positrons is simulated by means of an elaborate class II scheme in which hard interactions (involving deflection angles or energy transfers larger than pre-defined cutoffs) are simulated from the associated restricted differential cross sections. After a brief description of the interaction models adopted for photons and electrons/positrons, we describe the details of the class-II algorithm used for tracking electrons and positrons. The C++ classes are adapted to the specific code structure of GEANT4. They provide a complete description of the interactions and transport mechanics of electrons/positrons and photons in arbitrary materials, which can be activated from the G4ProcessManager to produce simulation results equivalent to those from the original PENELOPE programs. The combined code, named PENG4, benefits from the multi-threading capabilities and advanced geometry and statistical tools of GEANT4.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

A Comprehensive Investigation of Active Learning Strategies for Conducting Anti-Cancer Drug Screening

It is well-known that cancers of the same histology type can respond differently to a treatment. Thus, computational drug response prediction is of paramount importance for both preclinical drug screening studies and clinical treatment design. To build drug response prediction models, treatment response data need to be generated through screening experiments and used as input to train the prediction models. In this study, we investigate various active learning strategies of selecting experiments to generate response data for the purposes of (1) improving the performance of drug response prediction models built on the data and (2) identifying effective treatments. Here, we focus on constructing drug-specific response prediction models for cancer cell lines. Various approaches have been designed and applied to select cell lines for screening, including a random, greedy, uncertainty, diversity, combination of greedy and uncertainty, sampling-based hybrid, and iteration-based hybrid approach. All of these approaches are evaluated and compared using two criteria: (1) the number of identified hits that are selected experiments validated to be responsive, and (2) the performance of the response prediction model trained on the data of selected experiments. The analysis was conducted for 57 drugs and the results show a significant improvement on identifying hits using active learning approaches compared with the random and greedy sampling method. Active learning approaches also show an improvement on response prediction performance for some of the drugs and analysis runs compared with the greedy sampling method.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Hyperuniform and nearly hyperuniform random network materials

This invention is in the field of physical chemistry and relates to novel hyperuniform and nearly hyperuniform random network materials and methods of making said materials. Methods are described for controlling or altering the band gap of a material, and in particular commercially useful materials such as amorphous silicon. These methods can be exploited in the design of semiconductors, transistors, diodes, solar cells and the like.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Hyperuniform and nearly hyperuniform random network materials

This invention is in the field of physical chemistry and relates to novel hyperuniform and nearly hyperuniform random network materials and methods of making said materials. Methods are described for controlling or altering the band gap of a material, and in particular commercially useful materials such as amorphous silicon. These methods can be exploited in the design of semiconductors, transistors, diodes, solar cells and the like.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Optimization of Monte Carlo transport simulations in stochastic media

This paper presents an accurate and efficient approach to optimize radiation transport simulations in a stochastic medium of high heterogeneity, like the Very High Temperature Gas-cooled Reactor (VHTR) configurations packed with TRISO fuel particles. Based on a fast nearest neighbor search algorithm, a modified fast Random Sequential Addition (RSA) method is first developed to speed up the generation of the stochastic media systems packed with both mono-sized and poly-sized spheres. A fast neutron tracking method is then developed to optimize the next sphere boundary search in the radiation transport procedure. In order to investigate their accuracy and efficiency, the developed sphere packing and neutron tracking methods are implemented into an in-house continuous energy Monte Carlo code to solve an eigenvalue problem in VHTR unit cells. Comparison with the MCNP benchmark calculations for the same problem indicates that the new methods show considerably higher computational efficiency. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2010

Reexamination of the infrared properties of randomly stirred hydrodynamics

Dynamic renormalization-group (RG) methods were originally used by Forster, Nelson, and Stephen (FNS) to study the large-scale behavior of randomly stirred incompressible fluids governed by the Navier-Stokes equations. Similar calculations using a variety of methods have been performed but have led to a discrepancy in results. In this paper, we carefully reexamine in d dimensions the approaches used to calculate the renormalized viscosity increment and, by including an additional constraint which is neglected in many procedures, conclude that the original result of FNS is correct. By explicitly using step functions to control the domain of integration, we calculate a nonzero correction caused by boundary terms which cannot be ignored. We then go on to analyze how the noise renormalization, which is absent in many approaches, contributes an O(k{sup 2}) correction to the force autocorrelation and show conditions for this to be taken as a renormalization of the noise coefficient. Following this, we discuss the applicability of this RG procedure to the calculation of the inertial range properties of fluid turbulence.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

A semi-intrusive deterministic approach to uncertainty quantification in non-linear fluid flow problems

This paper deals with the formulation of a semi-intrusive (SI) method allowing the computation of statistics of linear and non linear PDEs solutions. This method shows to be very efficient to deal with probability density function of whatsoever form, long-term integration and discontinuities in stochastic space. Given a stochastic PDE where randomness is defined on Ω, starting from (i) a description of the solution in term of a space variables, (ii) a numerical scheme defined for any event ω∈Ω and (iii) a (family) of random variables that may be correlated, the solution is numerically described by its conditional expectancies of point values or cell averages and its evaluation constructed from the deterministic scheme. One of the tools is a tessellation of the random space as in finite volume methods for the space variables. Then, using these conditional expectancies and the geometrical description of the tessellation, a piecewise polynomial approximation in the random variables is computed using a reconstruction method that is standard for high order finite volume space, except that the measure is no longer the standard Lebesgue measure but the probability measure. This reconstruction is then used to formulate a scheme on the numerical approximation of the solution from the deterministic scheme. This new approach is said semi-intrusive because it requires only a limited amount of modification in a deterministic solver to quantify uncertainty on the state when the solver includes uncertain variables. The effectiveness of this method is illustrated for a modified version of Kraichnan–Orszag three-mode problem where a discontinuous pdf is associated to the stochastic variable, and for a nozzle flow with shocks. The results have been analyzed in terms of accuracy and probability measure flexibility. Finally, the importance of the probabilistic reconstruction in the stochastic space is shown up on an example where the exact solution is computable, the viscous Burgers equation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

DeepHyper: Asynchronous Hyperparameter Search for Deep Neural Networks

Hyperparameters employed by deep learning (DL) methods play a substantial role in the performance and reliability of these methods in practice. Unfortunately, finding performance-optimizing hyperparameter settings is a notoriously difficult task. Hyperparameter search methods typically have limited production-strength implementations or do not target scalability within a highly parallel machine, portability across different machines, experimental comparison between different methods, and tighter integration with workflow systems. In this paper, we present DeepHyper, a Python package that provides a common interface for the implementation and study of scalable hyperparameter search methods. It adopts the Balsam workflow system to hide the complexities of running large numbers of hyperparameter configurations in parallel on high-performance computing (HPC) systems. We implement and study asynchronous model-based search methods that consist of sampling a small number of input hyperparameter configurations and progressively fitting surrogate models over the input-output space until exhausting a user-defined budget of evaluations. We evaluate the efficacy of these methods relative to approaches such as random search, genetic algorithms, Bayesian optimization, and hyperband on DL benchmarks on CPU- and GPU-based HPC systems.

Balaprakash, Prasanna↗
DOE OSTI2016

LUNGx Challenge for computerized lung nodule classification

The purpose of this work is to describe the LUNGx Challenge for the computerized classification of lung nodules on diagnostic computed tomography (CT) scans as benign or malignant and report the performance of participants’ computerized methods along with that of six radiologists who participated in an observer study performing the same Challenge task on the same dataset. The Challenge provided sets of calibration and testing scans, established a performance assessment process, and created an infrastructure for case dissemination and result submission. We present ten groups that applied their own methods to 73 lung nodules (37 benign and 36 malignant) that were selected to achieve approximate size matching between the two cohorts. Area under the receiver operating characteristic curve (AUC) values for these methods ranged from 0.50 to 0.68; only three methods performed statistically better than random guessing. The radiologists’ AUC values ranged from 0.70 to 0.85; three radiologists performed statistically better than the best-performing computer method. The LUNGx Challenge compared the performance of computerized methods in the task of differentiating benign from malignant lung nodules on CT scans, placed in the context of the performance of radiologists on the same task. Lastly, the continued public availability of the Challenge cases will provide a valuable resource for the medical imaging research community.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Adaptation of the CVT algorithm for catheter optimization in high dose rate brachytherapy

Purpose: An innovative, simple, and fast method to optimize the number and position of catheters is presented for prostate and breast high dose rate (HDR) brachytherapy, both for arbitrary templates or template-free implants (such as robotic templates).Methods: Eight clinical cases were chosen randomly from a bank of patients, previously treated in our clinic to test our method. The 2D Centroidal Voronoi Tessellations (CVT) algorithm was adapted to distribute catheters uniformly in space, within the maximum external contour of the planning target volume. The catheters optimization procedure includes the inverse planning simulated annealing algorithm (IPSA). Complete treatment plans can then be generated from the algorithm for different number of catheters. The best plan is chosen from different dosimetry criteria and will automatically provide the number of catheters and their positions. After the CVT algorithm parameters were optimized for speed and dosimetric results, it was validated against prostate clinical cases, using clinically relevant dose parameters. The robustness to implantation error was also evaluated. Finally, the efficiency of the method was tested in breast interstitial HDR brachytherapy cases.Results: The effect of the number and locations of the catheters on prostate cancer patients was studied. Treatment plans with a better or equivalent dose distributions could be obtained with fewer catheters. A better or equal prostate V100 was obtained down to 12 catheters. Plans with nine or less catheters would not be clinically acceptable in terms of prostate V100 and D90. Implantation errors up to 3 mm were acceptable since no statistical difference was found when compared to 0 mm error (p > 0.05). No significant difference in dosimetric indices was observed for the different combination of parameters within the CVT algorithm. A linear relation was found between the number of random points and the optimization time of the CVT algorithm. Because the computation time decrease with the number of points and that no effects were observed on the dosimetric indices when varying the number of sampling points and the number of iterations, they were respectively fixed to 2500 and to 100. The computation time to obtain ten complete treatments plans ranging from 9 to 18 catheters, with the corresponding dosimetric indices, was 90 s. However, 93% of the computation time is used by a research version of IPSA. For the breast, on average, the Radiation Therapy Oncology Group recommendations would be satisfied down to 12 catheters. Plans with nine or less catheters would not be clinically acceptable in terms of V100, dose homogeneity index, and D90.Conclusions: The authors have devised a simple, fast and efficient method to optimize the number and position of catheters in interstitial HDR brachytherapy. The method was shown to be robust for both prostate and breast HDR brachytherapy. More importantly, the computation time of the algorithm is acceptable for clinical use. Ultimately, this catheter optimization algorithm could be coupled with a 3D ultrasound system to allow real-time guidance and planning in HDR brachytherapy.

61 RADIATION PROTECTION AND DOSIMETRY↗