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NASA NTRSDate not supplied

Icing Physics Studies Using the 3D SIDRM Test Article: Aerodynamic and Supercooled Liquid Icing Analysis

In-flight icing is an important safety issue and is a factor that affects aircraft design and performance. Newer regulations are driving a need for improvements in airframe and engine icing simulation capability. Experimental data is required for development of icing physics models and simulation validation. To that end, this paper presents the analysis of the supercooled liquid icing data subset from tests conducted in 2022 at the NASA Icing Research Tunnel that studied both supercooled water and ice-crystal icing. The test article that was utilized replicated 3D geometrical features of an inter-compressor duct and strut region of a turbofan engine. The surfaces of the Simulated Inter-compressor Duct Research Model (SIDRM) can be heated to simulate the warm surfaces of the turbofan inter-compressor duct. The test article is instrumented with pressure taps, heaters, heat flux gauges, and thermocouples, while a 3D laser scanner, cameras, and a scale to measure ice mass were utilized to characterize the icing behavior. The aim of these tests was to generate ice accretions on the SIDRM test article under well-characterized supercooled liquid icing and ice crystal icing conditions. This paper discusses measurements related to aerodynamic testing and supercooled liquid icing tests that were conducted. Aerodynamic measurements were analyzed and compared to computational simulations and were found to be in good agreement for the range of airspeeds (50 to 230 knots) and angles of attack (0 to 4°) tested. Various parametric sweeps were conducted during the supercooled liquid icing portion of the test entry (cloud median volumetric diameter ranged from 15 to 90 µm, total air temperature from -3 to -17 °C, angle of attack from 0 to 4°, and accretion time from 5 to 20 min). These sweeps were performed to measure that parameter’s impact on ice accretion size, location (icing extent), characteristics (such as glaze/rime ice and shedding behavior), and test article surface temperature. Analysis of the test data showed that clouds composed of larger drops, colder air temperatures, smaller angles of attack, and longer spray times were the primary parameters that resulted in accretions with greater ice mass. Test article angle of attack and cloud droplet size influenced the location of ice accretion as these two parameters directly impact collection efficiency. With respect to icing characteristics, total air temperature dictated icing type, and smaller cloud drop size along with warmer air temperatures resulted in greater amounts of ice shedding. Surface temperature increased during ice accretion from the release of latent (fusion) heat, where total air temperature and cloud drop size impacted the amount of surface temperature change. The icing measurements collected during the SIDRM tests will be used to develop and validate 3D computational engine icing tools, such as GlennICE, that predictively assesses the onset and growth of ice. One of the goals of the sponsoring NASA project is to develop simulation models and tools that can assist in the design and certification of engines for flight in icing conditions in a cost effective way.

supercooled liquid icing↗

DOE OSTI2024

Organochlorine pesticides and risk of papillary thyroid cancer in U.S. military personnel: a nested case-control study

Background: The effects of organochlorine pesticide (OCP) exposure on the development of human papillary thyroid cancer (PTC) are not well understood. A nested case-control study was conducted with data from the U.S. Department of Defense Serum Repository (DoDSR) cohort between 2000 and 2013 to assess associations of individual OCPs serum concentrations with PTC risk. Methods: This study included 742 histologically confirmed PTC cases (341 females, 401 males) and 742 individually-matched controls with pre-diagnostic serum samples selected from the DoDSR. Associations between categories of lipid-corrected serum concentrations of seven OCPs and PTC risk were evaluated for classical PTC and follicular PTC using conditional logistic regression, adjusted for body mass index category and military branch to compute odds ratios (OR) and 95% confidence intervals (CIs). Effect modification by sex, birth cohort, and race was examined. Results: There was no evidence of associations between most of the OCPs and PTC, overall or stratified by histological subtype. Overall, there was no evidence of an association between hexachlorobenzene (HCB) and PTC, but stratified by histological subtype HCB was associated with significantly increased risk of classical PTC (third tertile above the limit of detection (LOD) vs. <LOD, OR = 1.61, 95% CI, 1.09, 2.38; p for trend = 0.05) and significantly decreased risk of follicular variant PTC (third tertile above the limit of detection (LOD) vs. <LOD, OR = 0.38, 95% CI, 0.16, 0.91; p for trend = 0.04). Further stratified by sex, risk of classical PTC was higher for females (third tertile above LOD vs. <LOD, OR = 2.23, 95% CI: 1.23, 4.06; p-trend = 0.02) than for males (OR = 1.22, 95%CI: 0.72–2.08; p-trend = 0.56), though the test for interaction by sex was not statistically significant (p-interaction = 0.30). Similarly, β-hexachlorocyclohexane (β-HCCH) was associated with a higher risk for classical PTC for women with concentrations ≥LOD versus <LOD (OR = 1.76, 95% CI: 1.07, 2.89), while the effects were null for men. There were no consistent trends when stratified by race or birth year. Conclusions: The U.S. Environmental Protection Agency has classified HCB and other OCPs we studied here as probable human carcinogens. Our findings of increased risks for classical PTC associated with increased concentrations of HCB and β-HCCH, which were stronger among females, should be replicated in future studies of other populations.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

All-Atom Modeling and Simulation of Biopolymer Interface: Dual Role of Antifouling Polymer Brushes

Antifouling polymer brushes are well-known for their exceptional resistance to unwanted protein adsorption. While experimental studies have extensively characterized protein–polymer brush interactions, computational investigations remain limited, largely due to the challenges in accurately modeling and integrating these complex, multicomponent systems without resorting to oversimplification. To address this challenge, this study presents one of the most comprehensive and realistic model systems to date, comprising the substrate, grafted polymers, and proteins. Our work interprets the interactions between polymer brush and protein based on realistic modeling without simplification. In particular, this study utilizes molecular modeling and simulation of polycationic and polyzwitterionic brushes─poly(dimethylaminoethyl methacrylate) (PDMAEMA), poly(2-(N-oxide-N,N-dimethylamino)ethyl methacrylate) (PNOMA), and poly(2-(N-3-sulfopropyl-N,N-dimethylammonium)ethyl methacrylate) (PSBMA)─grafted onto α-quartz substrates via polymerization initiator linkers. The brush models were developed to closely replicate experimentally synthesized samples and to provide detailed insights into structural and dynamical changes at the molecular level during protein adsorption. Using steered molecular dynamics simulations, we show that the PSBMA brush, due to its high local density, exhibits the greatest resistance to protein insertion. Cα root-mean-square deviation and interaction pattern analyses further reveal that the PSBMA brush also induces the most significant destabilization of lysozyme, while the PDMAEMA brush enhances protein stability through ion-mediated interactions. The PNOMA brush, while requiring the lowest force for protein adsorption, induces greater protein destabilization than the PDMAEMA brush, primarily due to electrostatic repulsion caused by a short carbon spacer length. Hydration analysis reveals that both the PSBMA brush and the lysozyme interacting with it exhibit the most rapid dehydration, attributed to the brush’s high local chain density, which results in the greatest lysozyme destabilization and the highest adsorption force. These findings highlight the dual role of antifouling polymer brushes: resisting protein adsorption and modulating protein structural dynamics. In conclusion, this study provides valuable insights for the rational design of next-generation antifouling materials and offers a framework for realistic model development in complex multicomponent systems.

Adsorption↗

NASA NTRSDate not supplied

Feasibility Study of a Multi-Tilt-Rotor Aircraft as the Artemis Lunar Training Vehicle

The Lunar Landing Research Vehicles (LLRVs) and the Lunar Landing Training Vehicles (LLTVs) provided astronauts of the Apollo program with essential experience and confidence required to complete the missions, and contributed to six successful manned landings on the moon. The primary challenge in terrestrial training was being able to replicate the ratio of tilt angle to linear acceleration that a pilot would experience in lunar gravity. Presently, as the Artemis program seeks to return humans to the Moon by 2025, engineers are evaluating suitable platforms to serve as an In-Flight Trainer (IFT) or Artemis Lunar Training Vehicle (ALTV) for astronauts training in the task of manual landing. The program is investigating the viability of current technology in the field of electric vertical takeoff and landing (eVTOL) vehicles and is evaluating using a multi-tilt-rotor aircraft platform as a candidate for a preliminary ALTV. The tilt-rotor capability enables the vehicle attitude to be decoupled from its flight path, which is a crucial requirement in realistically simulating lunar gravity on Earth. Other key considerations include compensating for a lack of aerodynamic forces while flying through the atmosphere of Earth, as well as the ability to simulate the dynamics of multiple different lander designs for the Human Landing System (HLS) program. This paper details the feasibility study and presents a preliminary flight control architecture for an IFT based on a notional multi-tilt-rotor platform. The model-following control law, based on nonlinear dynamic inversion (NDI), removes the need for gain scheduling. The inner-loop dynamic control allocation strategy consists of a static portion that is optimized offline for trim while compensating for the difference in gravity and a dynamic portion that is computed in real time. The reference model consists of the full closed-loop dynamics of a generic HLS design. The modularity of the flight control architecture enables evaluation of multiple HLS concepts with minimal modifications to the control law. Simulation results of the multi-tilt-rotor configuration following the final portion of the Apollo 11 descent trajectory are shown.

Jing Pei↗

DOE OSTI2020

SIGNAL Game Manual

SIGNAL is a first of its kind experimental wargame developed as part of the Project on Nuclear Gaming (PoNG). In this document we describe the rules and game mechanics associated with the online version of SIGNAL created by team members from the University of California, Berkeley, Sandia National Laboratories, and Lawrence Livermore National Laboratory and sponsored by the Carnegie Corporation of New York. The game was developed as part of a larger research project to develop the experimental wargaming methodology and explore its use on a model scenario: the impact of various military capabilities on conflict escalation dynamics. We discuss the results of this research in a forthcoming paper that will include this manual as an appendix. It is our hope that this manual will both contribute to our players' understanding of the game prior to play and that it will allow for replication of the SIGNAL game environment for future research purposes. The manual begins by introducing the terminology used throughout the document. It then outlines the technical requirements required to run SIGNAL. The following section provides a description of the map, resources, infrastructure, tokens, and action cards used in the game environment. The manual then describes the user interface including the chat functions, trade mechanism, currency and population counts necessary for players to plan their actions. It then turns to the sequence of player actions in the game describing the signaling, action, and upkeep phases that comprise each round of play. It then outlines the use of diplomacy including alliances with minor states and trade between players. The manual also describes the process for scoring the game and determining the winner. The manual concludes with tips for players to remember as they embark upon playing the game.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Generative large language models for predictive maintenance planning

Maintenance planning and the generation of necessary components for tasks can prove time-consuming and complex. Automating the creation of recurring or similar tasks by leveraging previous planning packages and data, while uncovering insights to automate planning package generation, presents an opportunity to conserve valuable time and resources. This work aims to harness the textual and probabilistic capabilities of large language models (LLMs) to automate the generation of planning packages. Utilizing diverse data sources ranging from raw data to handwritten text, both singular and collaborative LLMs are trained and tested. Results demonstrate their capability to generate essential planning package components, effectively replicating the statistical patterns in the data. This demonstrates the use of these tools inside a digital asset for automated planning. This work outlines a methodology for constructing datasets, a training suite, and evaluation methods for LLM-based textual and conversational planning tools utilized in an asset digital twin. Results indicate that the fine-tuned models generate estimated planning information within the statistical ranges observed in real maintenance data. The models achieve high accuracy (>90%) in document question-answering and instruction generation tasks. Furthermore, the conversational retrieval-augmented generation (RAG) assistant system achieves 100% document retrieval accuracy, while conversational information capture exceeds 98% across the majority of work-package assistant modules.

97 MATHEMATICS AND COMPUTING↗

NASA NTRSDate not supplied

Feasibility Study of a Multi Tilt-rotor Aircraft as the Artemis Lunar Training Vehicle

The Lunar Landing Research Vehicles (LLRVs) and the Lunar Landing Training Vehicles (LLTVs) provided astronaut candidates for the Apollo program with essential experience and confidence required to complete the missions, and contributed to six successful manned landings on the moon. The primary challenge in terrestrial training was being able to replicate the ratio of bank angle to linear acceleration that a pilot would experience in lunar gravity. Presently, as the Artemis program seeks to return humans to the Moon by 2025, engineers are evaluating suitable platforms to serve as an In-Flight Trainer (IFT) or Artemis Lunar Training Vehicle (ALTV) for astronauts training in the task of manual landing. The program is investigating the viability of current technology in the field of electric vertical takeoff and landing (eVTOL) vehicles and is evaluating using a multi tilt-rotor aircraft platform as a candidate platform for a preliminary ALTV. The tilt-rotor capability enables the vehicle attitude to be decoupled from its flight path, which is a crucial requirement in realistically simulating lunar gravity on Earth. Other key considerations include compensating for a lack of aerodynamic forces while flying through the atmosphere of Earth, as well as the ability to simulate the dynamics of multiple different lander designs for the Human Landing System (HLS) program. This paper details the feasibility study and presents a preliminary flight control architecture for an IFT based on a notional multi tilt-rotor platform. The modeling-following control law, based on nonlinear dynamic inversion (NDI), removes the need for gain scheduling because the vehicle operates across a wide range of flight conditions. The inner-loop dynamic control allocation strategy consists of a static portion that is optimized offline for trim while compensating for the difference in gravity and a dynamic portion that is computed in real time. The reference model consists of the full closed-loop dynamics of a generic HLS design. The modularity of the flight control architecture enables evaluation of multiple HLS concepts with minimal modifications to the control law. Simulation results of the multi tilt-rotor configuration following the final portion of the Apollo 11 descent trajectory are shown.

Jing Pei↗

NASA NTRSDate not supplied

Icing Physics Studies Using the 3D SIDRM Test Article: Ice Crystal Icing Analysis

In-flight icing is an important safety issue and is a factor that affects aircraft design and performance. Newer regulations are driving a need for improvements in airframe and engine icing simulation capability. Experimental data is required for the development of icing physics models and simulation validation. This paper presents the analysis of the ice crystal icing data subset from tests conducted in 2022 at the NASA Icing Research Tunnel that studied both supercooled liquid and ice-crystal icing. The test article that was utilized replicated 3D geometrical features of an inter-compressor duct and strut region of a turbofan engine. The surfaces of the Simulated Inter-compressor Duct Research Model (SIDRM) can be heated to simulate the warm surfaces of the turbofan inter-compressor duct. The test article is instrumented with pressure taps, heaters, heat flux gauges, and thermocouples, while a 3D laser scanner, cameras, and a weighing scale to measure ice mass were utilized to characterize the icing behavior. The aim of these tests was to generate ice accretions on the SIDRM test article under well-characterized icing conditions. To that end, ice crystal cloud characterization tests were conducted that provided cloud property values at the test section. The ice crystal accretion tests investigated how different test condition parameters impacted ice accretion size, location, and characteristics (such as physical attributes). A key finding was that a sufficiently high surface heat flux at the leading edge can provide a continuous supply of liquid melt to critical accretion zones downstream, resulting in elevated ice mass accretions. Another key finding was that warmer heater settings in critical accretion zones can suppress ice accretion. These findings are consistent with icing behavior observed in full-scale engine icing tests conducted previously at the NASA Glenn Research Center. Test runs investigating the contribution of liquid melt generated at the leading edge found that the melt can be transported downstream to critical accretion regions in two forms, via runback and splash. The form of melt supplied downstream affected accretion behavior and features. Sharkteeth-shaped ice accretions were generated at certain test conditions, a physical attribute that has been observed in full-scale engine icing tests. The ice accretion data will be used to develop and validate 3D computational engine icing tools, such as GlennICE, that predictively assesses the onset and growth of ice. One of the goals of the sponsoring NASA project is to develop simulation models and tools that can assist in the design and certification of engines for flight in icing conditions in a cost‑effective way.

ice crystal icing↗

NASA NTRSDate not supplied

Icing Physics Studies Using the 3D SIDRM Test Article: Ice Crystal Icing Analysis

In-flight icing is an important safety issue and is a factor that affects aircraft design and performance. Newer regulations are driving a need for improvements in airframe and engine icing simulation capability. Experimental data is required for the development of icing physics models and simulation validation. This paper presents the analysis of the ice crystal icing data subset from tests conducted in 2022 at the NASA Icing Research Tunnel that studied both supercooled liquid and ice-crystal icing. The test article that was utilized replicated 3D geometrical features of an inter-compressor duct and strut region of a turbofan engine. The surfaces of the Simulated Inter-compressor Duct Research Model (SIDRM) can be heated to simulate the warm surfaces of the turbofan inter-compressor duct. The test article is instrumented with pressure taps, heaters, heat flux gauges, and thermocouples, while a 3D laser scanner, cameras, and a weighing scale to measure ice mass were utilized to characterize the icing behavior. The aim of these tests was to generate ice accretions on the SIDRM test article under well-characterized icing conditions. To that end, ice crystal cloud characterization tests were conducted that provided cloud property values at the test section. The ice crystal accretion tests investigated how different test condition parameters impacted ice accretion size, location, and characteristics (such as physical attributes). A key finding was that a sufficiently high surface heat flux at the leading edge can provide a continuous supply of liquid melt to critical accretion zones downstream, resulting in elevated ice mass accretions. Another key finding was that warmer heater settings in critical accretion zones can suppress ice accretion. These findings are consistent with icing behavior observed in full-scale engine icing tests conducted previously at the NASA Glenn Research Center. Test runs investigating the contribution of liquid melt generated at the leading edge found that the melt can be transported downstream to critical accretion regions in two forms, via runback and splash. The form of melt supplied downstream affected accretion behavior and features. Sharkteeth-shaped ice accretions were generated at certain test conditions, a physical attribute that has been observed in full-scale engine icing tests. The ice accretion data will be used to develop and validate 3D computational engine icing tools, such as GlennICE, that predictively assesses the onset and growth of ice. One of the goals of the sponsoring NASA project is to develop simulation models and tools that can assist in the design and certification of engines for flight in icing conditions in a cost‑effective way.

ice crystal icing↗

NASA NTRS2001

Analysis and visualization of single-trial event-related potentials

In this study, a linear decomposition technique, independent component analysis (ICA), is applied to single-trial multichannel EEG data from event-related potential (ERP) experiments. Spatial filters derived by ICA blindly separate the input data into a sum of temporally independent and spatially fixed components arising from distinct or overlapping brain or extra-brain sources. Both the data and their decomposition are displayed using a new visualization tool, the "ERP image," that can clearly characterize single-trial variations in the amplitudes and latencies of evoked responses, particularly when sorted by a relevant behavioral or physiological variable. These tools were used to analyze data from a visual selective attention experiment on 28 control subjects plus 22 neurological patients whose EEG records were heavily contaminated with blink and other eye-movement artifacts. Results show that ICA can separate artifactual, stimulus-locked, response-locked, and non-event-related background EEG activities into separate components, a taxonomy not obtained from conventional signal averaging approaches. This method allows: (1) removal of pervasive artifacts of all types from single-trial EEG records, (2) identification and segregation of stimulus- and response-locked EEG components, (3) examination of differences in single-trial responses, and (4) separation of temporally distinct but spatially overlapping EEG oscillatory activities with distinct relationships to task events. The proposed methods also allow the interaction between ERPs and the ongoing EEG to be investigated directly. We studied the between-subject component stability of ICA decomposition of single-trial EEG epochs by clustering components with similar scalp maps and activation power spectra. Components accounting for blinks, eye movements, temporal muscle activity, event-related potentials, and event-modulated alpha activities were largely replicated across subjects. Applying ICA and ERP image visualization to the analysis of sets of single trials from event-related EEG (or MEG) experiments can increase the information available from ERP (or ERF) data. Copyright 2001 Wiley-Liss, Inc.

Non-NASA Center↗

NASA NTRS2013

Science Opportunity Analyzer (SOA) Version 8

SOA allows scientists to plan spacecraft observations. It facilitates the identification of geometrically interesting times in a spacecraft s orbit that a user can use to plan observations or instrument-driven spacecraft maneuvers. These observations can then be visualized multiple ways in both two- and three-dimensional views. When observations have been optimized within a spacecraft's flight rules, the resulting plans can be output for use by other JPL uplink tools. Now in its eighth major version, SOA improves on these capabilities in a modern and integrated fashion. SOA consists of five major functions: Opportunity Search, Visualization, Observation Design, Constraint Checking, and Data Output. Opportunity Search is a GUI-driven interface to existing search engines that can be used to identify times when a spacecraft is in a specific geometrical relationship with other bodies in the solar system. This function can be used for advanced mission planning as well as for making last-minute adjustments to mission sequences in response to trajectory modifications. Visualization is a key aspect of SOA. The user can view observation opportunities in either a 3D representation or as a 2D map projection. Observation Design allows the user to orient the spacecraft and visualize the projection of the instrument field of view for that orientation using the same views as Opportunity Search. Constraint Checking is provided to validate various geometrical and physical aspects of an observation design. The user has the ability to easily create custom rules or to use official project-generated flight rules. This capability may also allow scientists to easily assess the cost to science if flight rule changes occur. Data Output allows the user to compute ancillary data related to an observation or to a given position of the spacecraft along its trajectory. The data can be saved as a tab-delimited text file or viewed as a graph. SOA combines science planning functionality unique to both JPL and the sponsoring spacecraft. SOA is able to ingest JPL SPICE Kernels that are used to drive the tool and its computations. A Percy search engine is then included that identifies interesting time periods for the user to build observations. When observations are then built, flight-like orientation algorithms replicate spacecraft dynamics to closely simulate the flight spacecraft s dynamics. SOA v8 represents large steps forward from SOA v7 in terms of quality, reliability, maintainability, efficiency, and user experience. A tailored agile development environment has been built around SOA that provides automated unit testing, continuous build and integration, a consolidated Web-based code and documentation storage environment, modern Java enhancements, and a focus on usability

Witoff, Robert J.↗

NASA NTRS1995

Real time acousto-ultrasonic NDE technique for monitoring damage in ceramic composites under dynamic loads

Research effort was directed towards developing a near real-time, acousto-ultrasonic (AU), nondestructive evaluation (NDE) tool to study the failure mechanisms of ceramic composites. Progression of damage is monitored in real-time by observing the changes in the received AU signal during the actual test. During the real-time AU test, the AU signals are generated and received by the AU transducers attached to the specimen while it is being subjected to increasing quasi-static loads or cyclic loads (10 Hz, R = 1.0). The received AU signals for 64 successive pulses were gated in the time domain (T = 40.96 micro sec) and then averaged every second over ten load cycles and stored in a computer file during fatigue tests. These averaged gated signals are representative of the damage state of the specimen at that point of its fatigue life. This is also the first major attempt in the development and application of real-time AU for continuously monitoring damage accumulation during fatigue without interrupting the test. The present work has verified the capability of the AU technique to assess the damage state in silicon carbide/calcium aluminosilicate (SiC/CAS) and silicon carbide/ magnesium aluminosilicate (SiC/MAS) ceramic composites. Continuous monitoring of damage initiation and progression under quasi-static ramp loading in tension to failure of unidirectional and cross-ply SiC/CAS and quasi-isotropic SiC/MAS ceramic composite specimens at room temperature was accomplished using near real-time AU parameters. The AU technique was shown to be able to detect the stress levels for the onset and saturation of matrix cracks, respectively. The critical cracking stress level is used as a design stress for brittle matrix composites operating at elevated temperatures. The AU technique has found that the critical cracking stress level is 10-15% below the level presently obtained for design purposes from analytical models. An acousto-ultrasonic stress-strain response (AUSSR) model for unidirectional and cross-ply ceramic composites was formulated. The AUSSR model predicts the strain response to increasing stress levels using real-time AU data and classical laminated plate theory. The Weibull parameters of the AUSSR model are used to calculate the design stress for thermo-structural applications. Real-time AU together with the AUSSR model was used to study the failure mechanisms of SiC/CAS ceramic composites under static and fatigue loading. An S-N curve was generated for a cross-ply SiC/CAS ceramic composite material. The AU results are corroborated and complemented by other NDE techniques, namely, in-situ optical microscope video recordings and edge replication.

Tiwari, Anil↗

DOE OSTI2023

A unified and constructive framework for the universality of neural networks

Abstract One of the reasons why many neural networks are capable of replicating complicated tasks or functions is their universal approximation property. Though the past few decades have seen tremendous advances in theories of neural networks, a single constructive and elementary framework for neural network universality remains unavailable. This paper is an effort to provide a unified and constructive framework for the universality of a large class of activation functions including most of the existing ones. At the heart of the framework is the concept of neural network approximate identity (nAI). The main result is as follows: any nAI activation function is universal in the space of continuous functions on compacta. It turns out that most of the existing activation functions are nAI, and thus universal. The framework induces several advantages over the contemporary counterparts. First, it is constructive with elementary means from functional analysis, probability theory, and numerical analysis. Second, it is one of the first unified and constructive attempts that is valid for most of the existing activation functions. Third, it provides new proofs for most activation functions. Fourth, for a given activation and error tolerance, the framework provides precisely the architecture of the corresponding one-hidden neural network with a predetermined number of neurons and the values of weights/biases. Fifth, the framework allows us to abstractly present the first universal approximation with a favorable non-asymptotic rate. Sixth, our framework also provides insights into the developments, and hence providing constructive derivations, of some of the existing approaches.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Machine Learning Analysis of Direct Dynamics Trajectory Outcomes for Thermal Deazetization of 2,3-Diazabicyclo[2.2.1]hept-2-ene

Experimentally, the thermal gas-phase deazetization of 2,3-diazabicyclo[2.2.1]hept-2-ene (1) results in the loss of N2 and the formation of bicyclo products 3 (exo) and 4 (endo) in a nonstatistical ratio, with preference for the exo product. Here, we report unrestricted M06-2X quasiclassical trajectories initialized from the concerted N2 ejection transition state that were able to replicate the experimental preference to form 3. We found that the 3:4 ratio results from the relative amounts of very fast (ballistic) exotype trajectories versus trajectories that lead to the 1,3-diradical intermediate 2. These quasiclassical trajectories provided a set of transition-state vibrational, velocity, momenta, and geometric features for the machine learning analysis. Additionally, a selection of popular supervised classification algorithms (e.g., random forest) provided poor prediction of trajectory outcomes based on only transition-state vibrational quanta and energy features. However, these machine learning models provided more accurate predictions using atomic velocities and atomic positions, attaining ~70% accuracy using initial conditions and between 85 and 95% accuracy at later reaction time steps. This increased accuracy allowed the feature importance analysis to reveal that, at the later-time analysis, the methylene bridge out-of-plane bending is correlated with trajectory outcomes for the formation of either the exo product or toward the diradical intermediate. Possible reasons for the struggle of machine learning algorithms to classify trajectories based on transition-state features is the heavily overlapping feature values, the finite but very large possible vibrational mode combinations, and the possibility of chaos as trajectories propagate. We examined this chaos by comparing a set of nearly identical trajectories that differed by only a very small scaling of the kinetic energies resulting from the transition-state reaction coordinate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRSDate not supplied

Benchmarking Computational Tools for Calling SNPs and Indels in Complex Microbial Populations

The NASA BioNutrients missions seek to understand the suitability of microorganisms for bioproduction during space flight. One topic of interest is the stability of microbial genomes during long-term ambient storage and subsequent rehydration and growth. To address these questions, samples from 8 species were flown to ISS for 5 years of desiccated storage at ambient temperature (Stasis Packs) and 2 species were packaged along with powdered media inside a bioreactor system to allow hydration and growth in microgravity (Production Packs). For both systems, Whole Genome Sequencing (WGS) of the DNA extracted from the returned samples and paired ground controls will be conducted to identify changes in genome stability due to time, storage conditions and growth in space. Across the technical replicates, ground controls, 10 timepoints, and multiple experimental conditions, ~300 samples have been selected for initial analysis with WGS sequencing to 100x coverage. A flexible and resource efficient mutation calling pipeline is needed to process this large dataset and allow for comparisons between species. Many bioinformatics tools for calling Indels and Single Nucleotide Variants (SNVs) are designed for use with pure isolates, where true variations from the reference genome are expected to dominate the reads aligning to the location of mutation. In contrast, DNA from the Stasis Pack (SP) samples was collected directly after recovery from desiccated storage and the Production Pack (PP) samples were collected after fermentation. In this context, reads with mutations are expected to be less frequent than reads that align with the reference genome, as each sample will include multiple lines of cells. Thus, BioNutrients samples are expected to be similar to samples from cancer cell or “pooled” sequencing approaches. In preparation for the analysis of the BioNutrients samples, we have tested three mutation calling tools (GATK for Microbes, BreSeq and DiscoSNP) designed for complex samples. A challenge of validating mutation identification pipelines is a lack of “Ground Truth” datasets, especially for complex samples. To compare these three tools, we sought to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO as part of the Space Algae-1 mission. Here we present a summary of these tools against the analysis originally conducted using the CRISP tool. Critical metrics are compared such as runtime, the number of SNPs, the number and size of Indels, and patterns of transversion and transitions identified by each tool are reported. By sharing these benchmarking results collected in support of the BioNutrients mission, we aim to guide others seeking to identify SNVs in similarly complex microbial samples.

Biology↗

NASA NTRS1999

Modeling the Activity of Single Genes

The central dogma of molecular biology states that information is stored in DNA, transcribed to messenger RNA (mRNA) and then translated into proteins. This picture is significantly augmentated when we consider the action of certain proteins in regulating transcription. These transcription factors provide a feedback pathway by which genes can regulate one another's expression as mRNA and then as protein. To review: DNA, RNA and proteins have different functions. DNA is the molecular storehouse of genetic information. When cells divide, the DNA is replicated, so that each daughter cell maintains the same genetic information as the mother cell. RNA acts as a go-between from DNA to proteins. Only a single copy of DNA is present, but multiple copies of the same piece of RNA may be present, allowing cells to make huge amounts of protein. In eukaryotes (organisms with a nucleus), DNA is found in the nucleus only. RNA is copied in the nucleus then translocates(moves) outside the nucleus, where it is transcribed into proteins. Along the way, the RNA may be spliced, i.e., may have pieces cut out. RNA then attaches to ribosomes and is translated to proteins. Proteins are the machinery of the cell other than DNA and RNA, all the complex molecules of the cell are proteins. Proteins are specialized machines, each of which fulfills its own task, which may be transporting oxygen, catalyzing reactions, or responding to extracellular signals, just to name a few. One of the more interesting functions a protein may have is binding directly or indirectly to DNA to perform transcriptional regulation, thus forming a closed feedback loop of gene regulation. The structure of DNA and the central dogma were understood in the 50s; in the early 80s it became possible to make arbitrary modifications to DNA and use cellular machinery to transcribe and translate the resulting genes; more recently, genomes (i.e., the complete DNA sequence) of many organisms have been sequenced. This large-scale sequencing began with simple organisms, viruses and bacteria, progressed to eukaryotes such as yeast, and more recently (1998) progressed to a multi-cellular animal, the nematode Caenorhabditis elegans. Sequencers have now moved on to the fruit fly Drosophila melanogaster, whose sequence is slated for completion by the end of 1999. The human genome project is expected to determine the complete sequence of all 3 billion bases of human DNA within the next five years. In the wake of genome-scale sequencing, further instrumentation is being developed to assay gene expression and function on a comparably large scale. Much of the work in computational biology focuses on computational tools used in sequencing, finding genes that are related to a particular gene, finding which parts of the DNA code for proteins and which do not, understanding what proteins will be formed from a given length of DNA, predicting how the proteins will fold from a one-dimensional structure into a three dimensional structure, and so on. Much less computational work has been done regarding the function of proteins. One reason for this is that different proteins function very differently, and so work on protein function is very specific to certain classes of proteins. There are, for example, proteins such enzymes that catalyze various intracellular reactions, receptors that respond to extracellular signals and ion channels that regulate the flow of charged particles into and out of the cell. In this chapter, we will consider a particular class of proteins called transcription factors(TFs), which are responsible for regulating when a certain gene is expressed in a certain cell, which cells it is express in, and how much is expressed. Understanding these processes will involve developing a deeper understanding of transcription, translation, and the cellular processes that control those processes. All of these elements fall under the aegis of gene regulation or more narrowly transcriptional regulation. Some of the key questions in gene regulation are: What genes are expressed in a certain cell at a certain time? How does gene expression differ from cell to cell in a multicellular organism? Which proteins act as transcription factors, i.e., are important in regulating gene expression? From questions like these, we hope to understand which genes are important for various macroscopic processes. Nearly all of the cells of a multicellular organism contain the same DNA. Yet this same genetic information yields a large number of different cell types. The fundamental difference between a neuron and a liver cell, for example, is which genes are expressed. Thus understanding gene regulation is an important step in understanding development. Furthermore, understanding the usual genes that are expressed in cells may give important clues about various diseases. Some diseases, such as sickle cell anemia and cystic fibrosis, are caused by defects in single, non-regulatory genes; others, such as certain cancers, are caused when the cellular control circuitry malfunctions - an understanding of these diseases will involve pathways of multiple interacting gene products. There are numerous challenges in the area of understanding and modeling gene regulation. First and foremost, biologists would like to develop a deeper understanding of the processes involved, including which genes and families of genes are important, how they interact, etc. From a computation point of view, there has been embarrassingly little work done. In this chapter there are many areas in which we can phrase meaningful, non-trivial computational questions, but questions that have not been addressed. Some of these are purely computational (what is a good algorithm for dealing with a model of type X) and others are more mathematical (given a system with certain characteristics, what sort of model can one use? How does one find biochemical parameters from system-level behavior using as few experiments as possible?). In addition to biological and algorithmic problems, there is also the ever-present issue of theoretical biology - what general principles can be derived from these systems, what can one do with models other than just simulate time-courses, what can be deduced about a class of systems without knowing all the details? The fundamental challenge to computationalists and theorists is to add value to the biology - to use models, modeling techniques and algorithms to understand the biology in new ways.

Mjolsness, Eric↗

DOE OSTI2026

Validation and Verification of Python based Neutron Spectrum Unfolding Software

To validate and verify the python-based code (PySL), designed to replicate the programs used by STAYSL for Beam Correction Factor (BCF) and Self-Shielding Factor (SHIELD), a series of tests were performed. To test BCF a python script was written to generate a random flux history file and both versions of the code processed the data. The test verified matching values up to at least one decimal place, approximately 10,000 tests where run and each one passed. Isotopes began to fail the tests once neutron saturation was reached. To verify this the total time of exposure was varied the isotopes that failed were compared to a list of their half-lives. The test process for SHIELD was very similar but, in this case, the code began by producing an input file with varying thickness and device type/environment for the SHIELD input. The failure condition for this test was if any of the data points for an isotope had a difference above 3%. Approximately 40 of these tests were run and there were only 3 isotopes that had reoccurring failures but only 2% of their points were above the 3% difference. A visual comparison was conducted by plotting the results from both programs. Although the test failed, the differences between their values were minuscule, and the self-shielding factor’s shape was preserved when plotted. Next steps for this project will be validating and verifying the python-based SigPhi code and then reproducing and testing the least squares unfolding performed by STAYSL.

73 - NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2007

Primary Objective Grating Astronomical Telescope

It has been 370 years since a seventeenth century French mathematician, Mersenne, presciently sketched out an astronomical telescope based on dual parabolic reflectors. Since that time the concept of the primary objective has been virtually unchanged. Now a new class of astronomical telescope with a primary objective grating (POG) has been studied as an alternative. The POG competes with mirrors, in part, because diffraction gratings provide the very chromatic dispersion that mirrors defeat. The resulting telescope deals effectively with long-standing restrictions on multiple object spectroscopy (MOS). Other potential benefits include unprecedented apertures and collection areas. The new design also favors space deployment as a gossamer membrane. The inventor, Tom Ditto, first discovered that higher-order diffraction images contain hidden depth cues, for which he was granted a seminal range finding patent in 1987. Subsequently, he invented and patented 3D localizers, profilometers and microscopes using POGs. The POG telescope was placed in the public domain to expedite research. The function of a telescopes primary objective is to collect flux and to deliver images. Both functions dictate that size matters, and bigger is better. For that reason, there has been a steady push over the past century to ramp up the size of the primary mirror. However, for every doubling of mirror diameter, the elapsed time between initial effort and first light has also doubled. Meanwhile, costs escalated beyond the mirror alone, because larger instruments required larger enclosures and better pointing mechanisms. One key catalog of observation, spectrographic data, is far more difficult to amass than two-dimensional imagery. While the number of observable objects has increased with mirror size, the capacity to take spectra has not increased proportionately. In the best of circumstances, spectrograms are available for one per cent of the all objects surveyed. Spectroscopy was a historical afterthought introduced in the nineteenth century shortly after the invention of the diffraction grating and over a century after Newtons 1670 telescope. Spectroscopy is generally accomplished using a diffraction grating as the disperser in the secondary. The light being delivered to the spectrograph is first captured by a primary mirror which provides no chromatic magnification by itself. Sizeable spectrographs could not be deployed while diffraction gratings were rare commodities scribed using mechanical ruling engines that produced one grating line at a time. Today diffraction gratings are commonplace. Their recent availability is a product of both the invention of holography and the mass replication of surface microstructures. Holography permits all lines in a grating to be made simultaneously in a single photographic exposure. Holograms can then be reproduced by embossing processes. The improvement in replication is analogous to how Gutenberg changed the availability of books. The masters may be expensive, but the copies are not. Computer science is another technology that emerged in the second half of the twentieth century without which our proposed spectrographic instrument could not function due to the complexity of image processing required in data reduction. The employment of very large diffraction gratings as primary objectives for astronomical telescopes requires a novel

spectroscopy↗