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At least 19 records

GL4U: GeneLab for Colleges and Universities

GeneLab for Colleges and Universities (GL4U) will provide space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab (GL) team will host two annual data processing bootcamps, one for college-level students (direct) and one for college educators (indirect – Training of Trainers), in which participants learn to analyze space-relevant omics data hosted on GL. The first bootcamp took place in early June 2021 with about 30 SJSU undergraduate students and covered space biology-specific lectures and hands-on instruction using Jupyter Notebooks (JNs) for RNA sequence (RNAseq) data analysis. All training materials including the enclosed files listed below will be made publicly available on GitHub. RNAseq Bootcamp Lectures (attached in combined file): Introduction to NASA, Space Biology, GeneLab, and the Command Line: NASA_GL_CL_Intro_FINAL.pdf - DRAFT from initial submission NASA_SB_GL_CL_Intro_FULL.pdf - FINAL version presented during the bootcamp - only minor edits from the draft version RNAseq and Data Processing Overview: RNAseq_Overview_FINAL.pdf - DRAFT from initial submission RNAseq_Overview_FULL.pdf - FINAL version presented during the bootcamp - only minor edits from the draft version Overview of the Statistics Used for RNAseq Data Analysis: SJSU_Statistics_Intro_Lecture_FINAL.pdf - DRAFT from initial submission Statistics_Overview_FULL.pdf - FINAL version presented during the bootcamp - only minor edits from the draft version Completed JNs in HTML format (attached in combined file): Unix_Intro_JN_06-2021_completed.html R_Intro_JN_06-2021_completed.html RNAseq_fastq_to_counts_JN_06-2021_completed.html RNAseq_DGE_JN_06-2021_completed.html RNAseq Bootcamp Recordings (attached): GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_1_of_5.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_2_of_5.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_3_of_5.mp4 *There were issues with the part 4 recording so that is not available GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_5_of_5.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day2_Part_1_of_3.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day2_Part_2_of_3.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day2_Part_3_of_3.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_1_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_2_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_3_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_4_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_1_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_2_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_3_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_4_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_1_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_2_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_3_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_4_of_4.mp4

GeneLab↗

Intermolecular potential for thermal H2O-He collisions

Theoretical potentials for rotational excitation of H2O by He were constructed via several methods, all of which start with a large basis set SCF interaction. The semiempirical Hartree-Fock with damped dispersion model adds a damped long-range attraction with parameters adjusted to fit experimental total differential cross sections. Purely ab initio potentials add correlation energies obtained via perturbation theory (MP2 and MP4) or a variational method (ICF1). Scattering calculations were performed on all surfaces to compare wih available beam scattering and pressure broadening data and to assess sensitivity of state-to-state rates to uncertainties in the potential. From comparison with the limited experimental data, the ICF1 surface appears to be marginally better than the MP4 surface. Thermal rates calculated from this surface should be accurate to better than 50 percent, at least for the larger, more important rates.

Palma, Amedeo↗

CN radical reactions with hydrogen cyanide and cyanogen - Comparison of theory and experiment

The method of laser photolysis/laser-induced fluorescence is used to obtain absolute rate constants for CN radical reactions with HCN and C2N2. The rate constants were found to be temperature-dependent in the range 300-740 K and pressure independent in the range 100-600 Torr. Rice-Remsperger-Kassel-Marcus theory for both reactions employing the transition state parameters obtained by the BAC-MP4 method are made. These calculations yielded reasonable results for the CN + HCN reaction, predicting both the temperature dependence and pressure independence. No pressure effect was observed in the pressure range 100-1000 Torr at temperatures below 900 K, confirming the experimental results.

Yang, D. L.↗

Theoretical characterization of the potential energy surface for NH + NO

The potential energy surface (PES) for NH + NO was characterized using complete active space self-consistent field (CASSCF) gradient calculations to determine the stationary point geometries and frequencies followed by CASSCF/internally contracted configuration interaction (CCI) calculations to refine the energetics. The present results are in qualitative accord with the BAC-MP4 calculations, but there are differences as large as 8 kcal/mol in the detailed energetics. Addition of NH to NO on a (2)A' surface, which correlated with N2 + OH or H + N2O products, involves barriers of 3.2 kcal/mol (trans) and 6.3 kcal/mol (cis). Experimental evidence for these barriers is found in earlier works. The (2)A' surface has no barrier to addition, but does not correlate with products. Surface crossings between the barrierless (2)A' surface and the (2)A' surface may be important. Production of N2 + OH products is predicted to occur via a planar saddle point of (2)A' symmetry. This is in accord with the preferential formation of II(A') lambda doublet levels of OH in earlier experiments. Addition of NH (1)delta to NO is found to occur on an excited state surface and is predicted to lead to N2O product as observed in earlier works.

Walch, Stephen P.↗

Theoretical characterization of the potential energy surface for NH + NO

The potential energy surface for NH + NO was characterized using complete active space self-consistent field (CASSCF) gradient calculation to determine the stationary point geometries and frequencies followed by CASSCF/internally contracted configuration interaction calculations to refine the energetics. The present results are in qualitative accord with the BAC-MP4 calculations, but there are differences as large as 8 kcal/mol in the detailed energetics.

Walch, Stephen P.↗

Cognitive Sciences

Session MP4 includes short reports on: (1) Face Recognition in Microgravity: Is Gravity Direction Involved in the Inversion Effect?; (2) Motor Timing under Microgravity; (3) Perceived Self-Motion Assessed by Computer-Generated Animations: Complexity and Reliability; (4) Prolonged Weightlessness Reference Frames and Visual Symmetry Detection; (5) Mental Representation of Gravity During a Locomotor Task; and (6) Haptic Perception in Weightlessness: A Sense of Force or a Sense of Effort?

Source record↗

Formation of Carbon Nanotube Based Gears: Quantum Chemistry and Molecular Mechanics Study of the Electrophilic Addition of o-Benzyne to Fullerenes, Graphene, and Nanotubes

Considerable progress has been made in recent years in chemical functionalization of fullerene molecules. In some cases, the predominant reaction products are different from those obtained (using the same reactants) from polycyclic aromatic hydrocarbons (PAHs). One such example is the cycloaddition of o-benzyne to C60. It is well established that benzyne adds across one of the rings in naphthalene, anthracene and other PAHs forming the [2+4] cycloaddition product (benzobicyclo[2.2.2.]-octatriene with naphthalene and triptycene with anthracene). However, Hoke et al demonstrated that the only reaction path for o-benzyne with C60 leads to the [2+2] cycloaddition product in which benzyne adds across one of the interpentagonal bonds (forming a cyclobutene ring in the process). Either reaction product results in a loss of aromaticity and distortion of the PAH or fullerene substrate, and in a loss of strain in the benzyne. It is not clear, however, why different products are preferred in these cases. In the current paper, we consider the stability of benzyne-nanotube adducts and the ability of Brenner's potential energy model to describe the structure and stability of these adducts. The Brenner potential has been widely used for describing diamondoid and graphitic carbon. Recently it has also been used for molecular mechanics and molecular dynamics simulations of fullerenes and nanotubes. However, it has not been tested for the case of functionalized fullerenes (especially with highly strained geometries). We use the Brenner potential for our companion nanogear simulations and believe that it should be calibrated to insure that those simulations are physically reasonable. In the present work, Density Functional theory (DFT) calculations are used to determine the preferred geometric structures and energetics for this calibration. The DFT method is a kind of ab initio quantum chemistry method for determining the electronic structure of molecules. For a given basis set expansion, it is comparable in accuracy to the MP2 method (better than Hartree Fock, but less accurate than more extensive electron correlation methods such as MP4 or CCSD). However, for systems with large numbers of basis functions it more efficient than any other methods that include electron correlation effects. In this presentation we show the results of DFT calculations for the reaction of benzyne with naphthalene, C60, and nanotube models. We compare energies for [2+2] and [2+4] cycloaddition products. The preferred products for the naphthalene and C60 reactions have been determined by experiment and, thus, these cases serve as a validation of our quantum chemical approach. We also compare the DFT and Brenner potential results. Finally we can predict the likelihood of reaction between benzyne and nanotubes.

Jaffe, Richard↗

Natural Language Processing (NLP) Analysis of NOTAMs for Air Traffic Management Optimization

With new emerging technologies in the field of NLP, we explore their applications to digitize and analyze heritage Air Traffic Management (ATM) documents for planning and optimizing airspace operations. Specifically, this research focuses on harvesting semi-structured or un-structured information contained in Notices to Airmen (NOTAMs). Using NLP and other advanced data analytics, we will construct a data-driven framework which facilitates finding language patterns and the use of pretrained language models for classification and extraction of useful airspace constraints and restrictions. These may lead to tools that assist airspace users in understanding the constraints more efficiently, contributing to better route planning and safer execution. This paper explores three workflows entailing different NLP tasks. First, unsupervised techniques like word embedding and topic modeling are used for pattern finding and document classification. Second, a dataset is created by extracting information from the semi-structured NOTAM format as metadata for categorizing, visualizing, and extracting key entities driving NOTAM content. Third, modern pre-built deep learning based transformer models such as BERT, RoBERTa, and XLNet are evaluated on the question answering task, an even more robust approach to information extraction, as well as their respective fine-tuning tasks. In this work we include various performance metrics for the trained models to evaluate both accuracy and precision and we show that the models can be generalized for their respective tasks. The research work developed shows promise in uncovering trends in digital NOTAMs in the NAS and also offers a new framework for digitizing and inferring insights from free-form legacy NOTAMs, that are yet to be digitized. Video is an mp4 download, with a play time of 9 min 35 secs.

Natural Language Processing↗

The “Gravity” of Combustion, Fluid and Soft Matter Research

Over the next year, the National Academies of Science, Engineering and Medicine (NASEM) will be developing the report for the next Decadal Survey on Life and Physical Sciences Research in space 2023-2032. This document will be used by the Science Mission Directorate in the National Aeronautics and Space Administration (NASA) to provide the framework for the vision, priorities, and strategic plan and budget for NASA’s research efforts in the area of biological and physical sciences in space, especially with regards to effects of gravity or the lack thereof. Gravity can affect fluid motion, shapes interfacial boundaries, squeezes compressible volumes by their surroundings, and ultimately affects heat and mass transfer as well as chemical reactions. NASEM will be requesting input from the research community via white papers in order to generate a comprehensive vision and strategy for a decade of transformative science at the frontiers of science space. Note: Accompanying videos are included in this submission and are listed based on there corresponding slide. For viewing you will need to download each mp4 formatted video, total run time 4 mins 2 secs. w/ color/sound.

combustion↗

What are Needed Innovations for Space Crop Production That May Also Benefit Vertical Farming?

I am speaking about the space crop production gaps and challenges we face and how we need innovations in the area of plant health monitoring, food safety contamination monitoring, CEA IPM, understanding of and manipulation of the microbiome/ecosystem, sustainability needs, novel sensors needed, automation and robotics, and also new crops that could be developed and ways that our needs parallel those of the vertical farming industry. (Note: This presentation is in video mp4 format is only viewable by download)

Gioia Massa↗

An Active Model Split for Hybrid RANS/LES of Compressible Flows

Hybrid RANS/LES models have consistently shown superior accuracy over RANS in predictions of massively separated flows. However, these models have experienced difficulties with modeled stress depletion, smooth-wall separated flow, and shock-separated flows. The Active Model Split (AMS) hybridization was created to address some of the fundamental shortcomings of traditional hybrid RANS/LES models. While previous work considered incompressible flows, this paper demonstrates how the AMS framework can be extended to address compressible flows. AMS-based hybrid models for the turbulent heat flux and turbulent transport terms in the total energy equation are presented. This compressible hybrid RANS/LES framework is demonstrated on a subsonic channel, a supersonic channel, and a transonic shock-boundary layer interaction. Record includes video of presentation, to view download the mp4 video attached run time of 10 mins 18 secs.

hybrid RANS/LES↗

Three-Dimensional Structure and Modeling of a Normal Bifurcated Shock Train from Experimental Measurements

An asymmetric, normal bifurcated shock train in a Mach 2 constant area, rectangular duct is investigated in the University of Michigan Direct Connect Isolator facility. High-speed schlieren imaging, wall static pressure measurements, surface oil flow visualization, and particle image velocimetry of the shock train are synthesized into a three-dimensional representation. This visualization is then used to inform the underlying flow physics of the distributed fluid dynamical processes along the shock train. The detailed, three-dimensional morphology of the flow profile entering the shock train is shown to have a significant impact on the separated flow morphology of the shock train. This results in a skewed supersonic core flow with alternating separation bubbles in the surrounding boundary layers. Finally, the efficacy of the prevailing pseudo-shock models in the literature is analyzed with the support of the available flow measurements. None are found to model both the pressure and streamwise Mach number profile of the UMDCI pseudo-shock. Note: This presentation is accompanied by the video presentation that can be downloaded for viewing and is formatted as an mp4 with a runtime of 10 min 15 secs.

Hypersonics↗

STEReO

STEReO brings together several technologies in Unmanned Aircraft Systems (UAS) Traffic Management (UTM), Autonomy, Communications, Human Factors, and Domain Expertise & Tools, aimed at providing scalability and flexibility, as well as operational resiliency to dynamic changes during a disaster event. Some of the concepts STEReO explores are: collaborative tools to ingest remote sensing information and distribute a common mission operating picture, apply ad-hoc communication networks to facilitate timely information sharing and communication of changes, vehicle-to-vehicle and onboard autonomy technologies ensure the safety and resiliency of operations, and apply NASA’s UAS traffic management system (UTM) as a public safety UAS Service Supplier (USS) to access and coordinate use of the airspace by both manned and unmanned operations. The potential benefits of STEReO include: standardized, cross-platform communication means increased interoperability and ease of cooperation/collaboration, increased situation awareness and common operating picture allow for earlier detection and decision making, and scalable to size and complexity of environment, operations, and mission objectives. This presentation gives an informational overview of the STEReO project to attendees of the Helicopter Association International (HAI) Aerial Firefighting Safety Conference. Note: Presentation slide 7 video is included in record as additional attachment, requires download of mp4 file, runtime 1 min 54 secs.

emergency response operations↗

NASA Ames Research Center Unitary Plan Wind Tunnel Fall 2018 Outage - Motor 1 Activity: Stator Shift

The Unitary Plan Wind Tunnel consists of the 11 x 11- Foot Transonic Wind Tunnel and the 9 x 7 foot Supersonic Wind Tunnel. The four 65,000hp electric motors that drive the wind tunnel compressors require periodic maintenance. In order to inspect the motors without the removal of drive shaft components, the stator must be shifted away from the motor. This process is referred to as "Stator Shift". Video is mp4 formatted with runtime of 2 mins 54 secs.

Wind Tunnel↗