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All sources NASA NTRS DOE OSTI

DOE OSTI2013

Quantitative assessment of biological impact using transcriptomic data and mechanistic network models

Exposure to biologically active substances such as therapeutic drugs or environmental toxicants can impact biological systems at various levels, affecting individual molecules, signaling pathways, and overall cellular processes. The ability to derive mechanistic insights from the resulting system responses requires the integration of experimental measures with a priori knowledge about the system and the interacting molecules therein. We developed a novel systems biology-based methodology that leverages mechanistic network models and transcriptomic data to quantitatively assess the biological impact of exposures to active substances. Hierarchically organized network models were first constructed to provide a coherent framework for investigating the impact of exposures at the molecular, pathway and process levels. We then validated our methodology using novel and previously published experiments. For both in vitro systems with simple exposure and in vivo systems with complex exposures, our methodology was able to recapitulate known biological responses matching expected or measured phenotypes. In addition, the quantitative results were in agreement with experimental endpoint data for many of the mechanistic effects that were assessed, providing further objective confirmation of the approach. We conclude that our methodology evaluates the biological impact of exposures in an objective, systematic, and quantifiable manner, enabling the computation of a systems-wide and pan-mechanistic biological impact measure for a given active substance or mixture. Our results suggest that various fields of human disease research, from drug development to consumer product testing and environmental impact analysis, could benefit from using this methodology. - Highlights: • The impact of biologically active substances is quantified at multiple levels. • The systems-level impact integrates the perturbations of individual networks. • The networks capture the relationships between the biological mechanisms. • Four exposure experiments have been assessed to validate the methodology. • The impact results were consistent with the corresponding phenotypic measures.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Computational study of ion beam extraction phenomena through multiple apertures

The process of ion extraction through multiple apertures is investigated using a two-dimensional particle-in-cell code. We consider apertures with a fixed diameter with a hydrogen plasma background, and the trajectories of electrons, H{sup +} and H{sub 2}{sup +} ions in the self-consistently calculated electric field are traced. The focus of this work is the fundamental physics of the ion extraction, and not particular to a specific device. The computed convergence and divergence of the extracted ion beam are analyzed. We find that the extracted ion flux reaching the extraction electrode is non-uniform, and the peak flux positions change according to operational parameters, and do not necessarily match the positions of the apertures in the y-direction. The profile of the ion flux reaching the electrode is mainly affected by the bias voltage and the distance between grid wall and extraction electrode.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1995

The use of cowl camber and taper to reduce rotor/stator interaction noise

The project had two specific technical objectives: (1) to develop a realistic three-dimensional model of tonal noise due to rotor/stator interaction, as the input field for predictions of diffraction and dissipation by a lined cowl; and (2) to determine whether the generator curve of that cowl, or duct, could be 'steered' to yield substantially lower values of propulsor noise along the engine's fore and aft open sectors. The more general and important aim of their research is to provide the commercial aircraft industry with a useful predictive tool to help it meet its noise-reduction goals. The work has produced a tractable and yet realistic model of rotor/stator interaction noise. The blades in the fan stage are radially divergent, twisted, and of realistically wide chords to match the high frequencies and speeds of the sound-production process. The resulting three-dimensional acoustic nearfield insonifies the interior wall of the diffracting cowl, whose shape, incidentally, does not affect fore or aft noise significantly (but other factors do).

Martinez, R.↗

NASA NTRS2009

Numerical Investigation of Plasma Flows in Magnetic Nozzles

Magnetic nozzles are used in many laboratory experiments in which plasma flows are to be confined, cooled, accelerated, or directed. At present, however, there is no generally accepted theoretical description that explains the phenomena of plasma expansion in and detachment from an externally-imposed magnetic field. The latter is an especially important problem in the field of plasma propulsion, where the ionized gas must detach from the applied, solenoidal magnetic field to realize thrust production. In this paper we simulate a plasma flowing in the presence of an applied magnetic field using a multidimensional numerical simulation tool that includes theoretical models of the various dispersive and dissipative processes present in the plasma. This is an extension of the simulation tool employed in previous work by Sankaran et al. The new tool employs the same formulation of the governing equation set, but retains the axial and radial components of magnetic field and the azimuthal component of velocity that were neglected. We aim to compare the computational results with the various proposed magnetic nozzle detachment theories to develop an understanding of the physical mechanisms that cause detachment. An applied magnetic field topology is obtained using a magnetostatic field solver, and this field is superimposed on the time-dependent magnetic field induced in the plasma to provide a self-consistent field description. The applied magnetic field and model geometry match those found in experiments by Kuriki and Okada. 4 A schematic showing the setup used in those experiments is shown. We model this geometry because there is a substantial amount of experimental data that can be compared to our computations, allowing for validation of the model. In addition, comparison of the simulation results with the experimentally obtained plasma parameters will provide insight into the mechanisms that lead to plasma detachment, revealing how they scale with different input parameters.

Sankaran, Kamesh↗

DOE OSTI2018

Crop Stem Width Estimation in Highly Cluttered Field Environment

We present two methods for estimation of crop stem width on small mobile robots. Stem width is an important phenotype needed by breeders and plant-biologists to measure plant growth, however, its manual measurement is cumbersome, in-accurate, and inefficient. The presented methods use a common image processing core that is designed to extract the foreground in the presence of significant leaf and stem clutter, view of other rows, and varying lighting, from a side-facing USB camera mounted on a small mobile robot. Using the extracted foreground, one approach uses estimates of robot velocity from wheel encoders and dense optical flow to estimate depth, while the other employs filtering of the LIDAR 2-D point cloud to estimate the depth. Both methods have been exhaustively validated against available hand-measurements on biomass sorghum (Sorghum bicolor) in real experimental fields. Experiments indicate that both methods are also applicable to other crops with cylindrical stems without significant modifications. The width estimation match on sorghum is 92.5% (using vision) and 98.2% (using vision and LIDAR) when compared against manual measurements by trained agronomists. Thus, our results clearly establish the feasibility of using small robots for stem-width estimation in realistic field settings. Furthermore, the techniques presented here can be utilized for automating other phenotypic measurements.

Choudhuri, Anwesa↗

DOE OSTI2011

Two Photon Absorption And Refraction in Bulk of the Semiconducting Materials

Fast electronic detection systems have opened up a number of new fields like nonlinear optics, optical communication, coherent optics, optical bistability, two/four wave mixing. The interest in this field has been stimulated by the importance of multiphoton processes in many fundamental aspects of physics. It has proved to be an invaluable tool for determining the optical and electronic properties of the solids because of the fact that one gets the information about the bulk of the material rather than the surface one. In this paper we report, the measurement of the nonlinear absorption and refraction from the band gap to half-band gap region of bulk of semiconductors in the direct and indirect band gap crystals with nanosecond laser. The measured theoretical calculated values of two-photon absorption coefficients ({beta}) and nonlinear refraction n{sub 2}({omega}) of direct band gap crystal match the earlier reported theoretical predictions. By making use of these theoretical calculated values, we have estimated {beta} and n{sub 2}({omega}) in the case of indirect band gap crystals. Low value of absorption coefficient in case of indirect band gap crystals have been attributed to phonon assisted transition while reduction in nonlinear refraction is due to the rise in saturation taking place in the absorption.

36 MATERIALS SCIENCE↗

DOE OSTI2016

The effectiveness of pretreatment physics plan review for detecting errors in radiation therapy

Purpose: The pretreatment physics plan review is a standard tool for ensuring treatment quality. Studies have shown that the majority of errors in radiation oncology originate in treatment planning, which underscores the importance of the pretreatment physics plan review. This quality assurance measure is fundamentally important and central to the safety of patients and the quality of care that they receive. However, little is known about its effectiveness. The purpose of this study was to analyze reported incidents to quantify the effectiveness of the pretreatment physics plan review with the goal of improving it. Methods: This study analyzed 522 potentially severe or critical near-miss events within an institutional incident learning system collected over a three-year period. Of these 522 events, 356 originated at a workflow point that was prior to the pretreatment physics plan review. The remaining 166 events originated after the pretreatment physics plan review and were not considered in the study. The applicable 356 events were classified into one of the three categories: (1) events detected by the pretreatment physics plan review, (2) events not detected but “potentially detectable” by the physics review, and (3) events “not detectable” by the physics review. Potentially detectable events were further classified by which specific checks performed during the pretreatment physics plan review detected or could have detected the event. For these events, the associated specific check was also evaluated as to the possibility of automating that check given current data structures. For comparison, a similar analysis was carried out on 81 events from the international SAFRON radiation oncology incident learning system. Results: Of the 356 applicable events from the institutional database, 180/356 (51%) were detected or could have been detected by the pretreatment physics plan review. Of these events, 125 actually passed through the physics review; however, only 38% (47/125) were actually detected at the review. Of the 81 events from the SAFRON database, 66/81 (81%) were potentially detectable by the pretreatment physics plan review. From the institutional database, three specific physics checks were particularly effective at detecting events (combined effectiveness of 38%): verifying the isocenter (39/180), verifying DRRs (17/180), and verifying that the plan matched the prescription (12/180). The most effective checks from the SAFRON database were verifying that the plan matched the prescription (13/66) and verifying the field parameters in the record and verify system against those in the plan (23/66). Software-based plan checking systems, if available, would have potential effectiveness of 29% and 64% at detecting events from the institutional and SAFRON databases, respectively. Conclusions: Pretreatment physics plan review is a key safety measure and can detect a high percentage of errors. However, the majority of errors that potentially could have been detected were not detected in this study, indicating the need to improve the pretreatment physics plan review performance. Suggestions for improvement include the automation of specific physics checks performed during the pretreatment physics plan review and the standardization of the review process.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2001

Evidence of Stratosphere-to-Troposphere Transport Within a Mesoscale Model and Total Ozone Mapping Spectrometer Total Ozone

We evaluate evidence for stratospheric mass transport into, and mass remaining in, the troposphere during an intense midlatitude cyclone. Mesoscale forecast model analysis fields from the Mesoscale Analysis and Prediction System were matched with total ozone observations from the Total Ozone Measurement Spectrometer. Combined with parcel back trajectory calculations, the analyses imply that two mechanisms contributed to the mass exchange: (1) An area of dynamically induced exchange was observed on the cyclone's southern edge. Parcels originally in the stratosphere crossed the jet core and were diluted through turbulent mixing with tropospheric air; (2) Diabetic effects reduced parcel potential vorticity (PC) for trajectories traversing precipitation regions, creating a 'PV hole' signature in the center of the cyclone. Air with characteristics of ozone and water vapor found in the lower stratosphere remained in the troposphere. The strength of the latter process may be unusual. Combined with other research, these results suggest that precipitation-induced diabetic effects can significantly modify (either decreasing or increasing) parcel potential vorticity, depending on parcel trajectory configuration with respect to maximum heating regions and jet core. The diabetic heating effect on stratosphere-troposphere exchange (STE) is more important to tropopause erosion than to altering parcel trajectories. In addition, these results underline the importance of using not only PC but also chemical constituents for diagnoses of STE.

Olsen, Mark A.↗

DOE OSTI2014

Memory Optimization for Phase-field Simulations

Phase-field simulations are computationally and memory intensive applications. Many of the phase-field simulations being conducted in support of NEAMS were not capable of running on “normal clusters” with 2-4GB of RAM per core, and instead required specialized “big-memory” clusters with 64GB per core. To address this issue, the MOOSE team developed a new Python-based utility called MemoryLogger, and applied it to locate, diagnose, and eradicate memory bottlenecks within the MOOSE framework. MemoryLogger allows for a better understanding of the memory usage of an application being run in parallel across a cluster. Memory usage information is captured for every individual process in a parallel job, and communicated to the head node of the cluster. Console text output from the application itself is automatically matched with this memory usage information to produce a detailed picture of memory usage over time, making it straightforward to identify the subroutines which contribute most to the application’s peak memory usage. The information produced by the MemoryLogger quickly and effectively narrows the search for memory optimizations to the most data-intensive parts of the simulation.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2019

Modeling the Formation of the Family of the Dwarf Planet Haumea

The dwarf planet (136108) Haumea has an intriguing combination of unique physical properties: near-breakup spin, two regular satellites, and an unexpectedly compact family. While these properties point toward formation by a collision, there is no self-consistent and reasonably probable formation hypothesis that can connect the unusually rapid spin and low relative velocities of Haumea family members (“Haumeans”). We explore and test the proposed formation hypotheses (catastrophic collision, graze-and-merge, and satellite collision) in detail. We flexibly parameterize the properties of the collision (e.g., the collision location) and use simple models for the unique three-dimensional velocity ejection field expected from each model to generate simulated families. These are then compared to the observed Kuiper Belt objects using Bayesian parameter inference, including a mixture model that robustly allows for interlopers from the background population. After testing our methodology, we find that the best match to the observed Haumeans is an essentially isotropic ejection field with a typical velocity of 150 m s{sup −1}. The graze-and-merge formation hypothesis—in which Haumeans are shed due to excess angular momentum—is clearly disfavored because the observed Haumeans are not oriented in a plane. The satellite collision model is also disfavored. Including these new constraints, we present a detailed discussion of the formation hypotheses, including variations, some of which are tested. Some new hypotheses are proposed (a cratering collision and a collision where Haumea’s upper layers are “missing”) and scrutinized. We do not identify a satisfactory formation hypothesis, but we do propose several avenues of additional investigation. In the process of these analyses, we identify many new candidate Haumeans and dynamically confirm seven of them as consistent with the observed family. We also confirm that Haumeans have a shallow size distribution and discuss implications for the discovery and identification of new Haumeans.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1991

Temporal variation of the earth's low-degree zonal gravitational field caused by atmospheric mass redistribution - 1980-1988

Temporal variations in the low-degree zonal harmonics of the earth's gravitational field have recently been observed by satellite laser ranging. A host of geophysical processes contribute to these variations. The present paper studies quantitatively a prime contributor, atmospheric mass redistribution, using ECMWF global surface pressure data for the period of 1980-1988. The annual and semiannual amplitudes and phases of the zonal J(l) coefficient with degree l = 2-6 with and without the oceanic inverted-barometer (IB) effect are computed to obtain the predicted effects on the orbit nodal residuals of Lageos and Starlette. These predicted values are then compared with observations. It is found that the atmospheric influence, combined with the hydrological influence agree well with the Lageos observation for the annual term. The corresponding match appears poorer for Starlette.

Chao, B. Fong↗

NASA NTRS2008

Microwave-to-Optical Conversion in WGM Resonators

Microwave-to-optical frequency converters based on whispering-gallery-mode (WGM) resonators have been proposed as mixers for the input ends of microwave receivers in which, downstream of the input ends, signals would be processed photonically. A frequency converter as proposed (see figure) would exploit the nonlinearity of the electromagnetic response of a WGM resonator made of LiNbO3 or another suitable ferroelectric material. Up-conversion would take place by three-wave mixing in the resonator. The WGM resonator would be de - signed and fabricated to obtain (1) resonance at both the microwave and the optical operating frequencies and (2) phase matching among the input and output microwave and optical signals as described in the immediately preceding article. Because the resonator would be all dielectric there would be no metal electrodes signal losses would be very low and, consequently, the resonance quality factors (Q values) of the microwave and optical fields would be very large. The long lifetimes associated with the large Q values would enable attainment of high efficiency of nonlinear interaction with low saturation power. It is anticipated that efficiency would be especially well enhanced by the combination of optical and microwave resonances in operation at input signal frequencies between 90 and 300 GHz.

Savchenkov, Anatoliy↗

DOE OSTI2020

Neutrino identification with scintillation light in MicroBooNE

MicroBooNE is a neutrino experiment which employs a liquid argon (LAr) time projection chamber (TPC) to record neutrino interactions from Fermilab's neutrino beamlines. The experiment's primary objective is to study low-energy νe interactions from the Booster Neutrino Beamline (BNB). Located on the surface, the detector is affected by a continuous rate of cosmic-rays. This leads to one neutrino interaction for every 104 cosmic rays observed in the TPC, making it difficult to isolate neutrino interactions in the detector using charge alone. MicroBooNE's trigger makes use of prompt scintillation light and plays an essential role in both performing strong background rejection and significantly reducing data-rates. Furthermore, a series of novel techniques relying on scintillation light are used to isolate beam-induced activity. This document briefly presents MicroBooNE's scintillation-light based trigger and novel Flash-Matching pattern recognition techniques for cosmic-rejection. This work serves as the foundation of neutrino analyses in LArTPC detectors and is therefore of interest to the broader short- and long-baseline neutrino programs being launched at Fermilab.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2010

Computational and experimental research on infrared trace by human being contact

The indoor detection of the human body's thermal trace plays an important role in the fields of infrared detecting, scouting, infrared camouflage, and infrared rescuing and tracking. Currently, quantitative description and analysis for this technology are lacking due to the absence of human infrared radiation analysis. To solve this problem, we study the heating and cooling process by observing body contact and removal on an object, respectively. Through finite-element simulation and carefully designed experiments, an analytical model of the infrared trace of body contact is developed based on infrared physics and heat transfer theory. Using this model, the impact of body temperature on material thermal parameters is investigated. The sensitivity of material thermal parameters, the thermal distribution, and the changes of the thermograph's contrast are then found and analyzed. Excellent matching results achieved between the simulation and the experiments demonstrate the strong impact of temperature on material thermal parameters. Conclusively, the new model, simulation, and experimental results are beneficial to the future development and implementation of infrared trace technology.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1989

Application of a single area array detector for acquistion, tracking and point-ahead in space optical communications

Functions of acquisition, tracking, and point-ahead in space optical communications are being combined into a single system utilizing an area array detector. An analysis is presented of the feasibility concept. The key parameters are: optical power less than 1 pW at 0.86 micrometer, acquisition in less than 30 seconds in an acquisition field of view (FOV) of 1 mrad, tracking with 0.5 microrad rms noise at 1000 Hz update rate, and point ahead transfer function precision of 0.25 microrad over a region of 150 microrad. Currently available array detectors were examined. The most demanding specifications are low output noise, a high detection efficiency, a large number of pixels, and frame rates over 1kHz. A proof of concept (POC) demonstration system is currently being built utilizing the Kodak HS-40 detector (a 128 x 128 photodiode array with a 64 channel CCD readout architecture which can be operated at frame rates as high as 40,000/sec). The POC system implements a windowing scheme and special purpose digital signal processing electronic for matched filter acquisition and tracking algorithms.

Clark, D. L.↗

NASA NTRS1989

Application of a single area array detector for acquisition, tracking and point-ahead in space optical communications

Clark, D. L.↗

NASA NTRS2007

Numerical Investigation of Plasma Flows in Magnetic Nozzles

Magnetic nozzles are used in many laboratory experiments in which plasma flows are to be confined, cooled. accelerated, or directed. At present, however, there is no generally accepted theoretical description that explains the phenomena of plasma detachment from an externally-imposed magnetic field. This is an important problem in the field of plasma propulsion, where the ionized gas must detach from the applied, solenoidal magnetic field to realize thrust production. In this paper we simulate a plasma flowing in the presence of an applied magnetic field using a multidimensional numerical simulation tool that includes theoretical models of the various dispersive and dissipative processes present in the plasma. This is an extension of the simulation tool employed in previous work by Sankaran et al. The new tool employs the same formulation of the governing equation set. but retains the axial and radial components of magnetic field and the azimuthal component of velocity that were neglected in other works. We aim to compare the computational results with the various proposed magnetic nozzle detachment theories to develop an understanding of the physical mechanisms that cause detachment. An applied magnetic field topology is obtained using a magnetostatic field solver and this field is superimposed on the time-dependent magnetic field induced in the plasma to provide a self-consistent field description. The applied magnetic field and model geometry match those found in experiments by Kurtki and Okada. We model this geometry because there ts a substantial amount of experimental data that can be compared to our computations, allowing for validation of the model. In addition, comparison of the simulation results with the experimentally obtained plasma parameters will provide insight into the mechanisms that lead to plasma detachment, revealing how the 3 scale with different input parameters.

Polzin, K. A.↗

NASA NTRS2008

Validation of High-Fidelity CFD Simulations for Rocket Injector Design

Computational fluid dynamics (CFD) has the potential to improve the historical rocket injector design process by evaluating the sensitivity of performance and injector-driven thermal environments to the details of the injector geometry and key operational parameters. Methodical verification and validation efforts on a range of coaxial injector elements have shown the current production CFD capability must be improved in order to quantitatively impact the injector design process. This paper documents the status of a focused effort to compare and understand the predictive capabilities and computational requirements of a range of CFD methodologies on a set of single element injector model problems. The steady Reynolds-Average Navier-Stokes (RANS), unsteady Reynolds-Average Navier-Stokes (URANS) and three different approaches using the Large Eddy Simulation (LES) technique were used to simulate the initial model problem, a single element coaxial injector using gaseous oxygen and gaseous hydrogen propellants. While one high-fidelity LES result matches the experimental combustion chamber wall heat flux very well, there is no monotonic convergence to the data with increasing computational tool fidelity. Systematic evaluation of key flow field regions such as the flame zone, the head end recirculation zone and the downstream near wall zone has shed significant, though as of yet incomplete, light on the complex, underlying causes for the performance level of each technique. 1 Aerospace Engineer and Combustion CFD Team Leader, MS ER42, NASA MSFC, AL 35812, Senior Member, AIAA. 2 Professor and Director, Computational Combustion Laboratory, School of Aerospace Engineering, 270 Ferst Dr., Atlanta, GA 30332, Associate Fellow, AIAA. 3 Reilly Professor of Engineering, School of Mechanical Engineering, 585 Purdue Mall, West Lafayette, IN 47907, Fellow, AIAA. 4 Principal Member of Technical Staff, Combustion Research Facility, 7011 East Avenue, MS9051, Livermore, CA 94550, Associate Fellow, AIAA. 5 J. L. and G. H. McCain Endowed Chair, Mechanical Engineering, 104 Research Building East, University Park, PA 16802, Fellow, AIAA. American Institute of Aeronautics and Astronautics 1

Tucker, P. Kevin↗