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Multi-User Space Link Extension (SLE) System

The Multi-User Space (MUS) Link Extension system, a software and data system, provides Space Link Extension (SLE) users with three space data transfer services in timely, complete, and offline modes as applicable according to standards defined by the Consultative Committee for Space Data Systems (CCSDS). MUS radically reduces the schedule, cost, and risk of implementing a new SLE user system, minimizes operating costs with a lights-out approach to SLE, and is designed to require no sustaining engineering expense during its lifetime unless changes in the CCSDS SLE standards, combined with new provider implementations, force changes. No software modification to MUS needs to be made to support a new mission. Any systems engineer with Linux experience can begin testing SLE user service instances with MUS starting from a personal computer (PC) within five days. For flight operators, MUS provides a familiar-looking Web page for entering SLE configuration data received from SLE. Operators can also use the Web page to back up a space mission's entire set of up to approximately 500 SLE service instances in less than five seconds, or to restore or transfer from another system the same amount of data from a MUS backup file in about the same amount of time. Missions operate each MUS SLE service instance independently by sending it MUS directives, which are legible, plain ASCII strings. MUS directives are usually (but not necessarily) sent through a TCP-IP (Transmission Control Protocol Internet Protocol) socket from a MOC (Mission Operations Center) or POCC (Payload Operations Control Center) system, under scripted control, during "lights-out" spacecraft operation. MUS permits the flight operations team to configure independently each of its data interfaces; not only commands and telemetry, but also MUS status messages to the MOC. Interfaces can use single- or multiple-client TCP/IP server sockets, TCP/IP client sockets, temporary disk files, the system log, or standard in, standard out, or standard error as applicable. By defining MUS templates in ASCII, the flight operations team can include any MUS system variable in telemetry or command headers or footers, and/or in status messages. Data fields can be arranged within messages in different sequences, according to the mission s needs. The only constraints imposed are on the format of MUS directive strings, and some bare minimum logical requirements that must be met in order for MUS to read the mission control center's spacecraft command inputs. The MUS system imposes no limits or constraints on the numbers and combinations of missions and SLE service instances that it will support simultaneously. At any time, flight operators may add, change, delete, bind, connect, or disconnect.

Perkins, Toby↗

In situ Detection of Plasma Induced Surface Interaction based on Deep Learning based Visual Diagnostics (Technical Report)

It is characteristic for many plasma devices to undergo plasma-material interaction leading to surface erosion. These processes, often not easily detectable, lead to changes in device performance and lifespan. State-of-the-art lifetime tests and wear experiments require over 1000s hours. A self-consistent model for accurately predicting the erosion's effects is not available. In situ detection of these processes is not a trivial task since the surface variations at the early stages have a micron scale. Such limitations not only restrict testing and prediction capabilities but also slow the development of new thrusters and limit mission duration. To address these challenges, an in-situ diagnostic for real-time erosion assessment has been developed, aiming to expedite lifetime testing and broaden experimental campaigns. Several works were dedicated to real-time and in situ monitoring of material erosion during plasma exposure using laser holography, microscopy, and with telemicroscopes. However, the applicability of these approaches is limited due to complexity, cost and less flexibility as they often require placing diagnostic equipment inside the vacuum chamber. In collaboration with Princeton Collaborative Research Facility (PCRF), Princeton Plasma Physics Laboratory (PPPL), a new diagnostic approach is developed, where geometry modifications to the ceramic channel walls were introduced that would result in accelerated channel erosion. We employed Long-distance microscope (LDM) imagery, combined with Deep-Learning based Shape from focus or depth from focus (DFF or SFF) approach, that provides an accessible and cost-effective solution. LDM employs focus variation techniques to continuously capture multiple images of the target object at distinct focal planes. DFF, an optical focus variation method, generates a 3D topographical surface depth map from a sequence of variably focused images. Combined with the developed diagnostic, this approach offers a controllable means to study erosion under accelerated conditions. In this work, we develop Neural Network-based DFF algorithm applicable for LDM data to quantitatively evaluate plasma induced surface modification from LDM data. Next, we develop Deep Learning-based super-resolution depth map image reconstruction technique to increase the resolution of depth maps obtained from DFF algorithm to improve the accuracy of erosion measurements. Thirdly, we develop several image processing techniques to remove noise and improve the quality of depth map image. Here we report the results of initial tests for this approach. An experimental setup designed and built in PPPL was employed that consists of a 3-cm gridded ion source that produces a neutralized argon beam with energies up to 600 eV. A hexagonal boron nitride (h-BN) ceramic target, designed based on computational predictions, was used. Tests were conducted to reconstruct the complex geometry of the target under the lighting conditions of the operated ion source.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

FTIR Analysis of Water in Pyroxene and Plagioclase in ALH 84001 and Nakhlites

Determining the volatile budget of the interior of Mars is crucial for our understanding of that planet's formation, geodynamics, cooling history and the origin of its volcanism and atmosphere as well as its potential for life. Surficial water is evident from spacecraft and rover data in polar caps and the atmosphere, in the presence of river channels, and in the detection of water-bearing minerals. Meteorites, however, are our best candidates for estimating the amount of water present at depth, even if all are crustal samples. The last 10 years have seen a blooming of studies measuring water and halogens in Martian meteorites. The bulk of these studies target phosphate, a typically late-stage phase in the igneous Martian meteorites that potentially would concentrate incompatible element hydrogen (H quantified traditionally as "water", i.e., H2O concentrations in weight) near the end of the crystallization sequence. However, determining the amount of water, F, and Cl in the magma from which a phosphate crystallized from is not straightforward and in most instances not possible. On the other hand, phosphates have turned out to be very useful in identifying hydrothermal processes that could have added water while or after the magma flowed and crystallized. Another caveat of analyzing Martian meteorite phases for water is that shocked phases such as maskelynite and impact melts appear to have incorporated water from the Martian atmosphere, as evidenced by high H isotope ((delta)D) signatures, and therefore their water concentrations cannot be interpreted in terms of deep planetary processes. The best candidates for estimating the water content of the Martian interior have been melt inclusions (glass or amphibole-bearing) which the enclosing mineral (usually olivine) would have prevented from exchanging volatiles with the surroundings after crystallization. Even some of these, however, have high (delta)D, meaning they were affected by H exchange via impact events or with crustal reservoirs or hydrothermal fluids. Here, nominally anhydrous minerals (pyroxene, olivine, plagioclase, or maskelynite) in orthopyroxenite ALH 84001 and selected nakhlites are analyzed for water and major elements, in order to determine 1) whether they contain any water; 2) if they do, what controls its distribution (crystallization, degassing, hydrothermal or impact processes); and 3) if any of these measurements can be used to infer the water contents of the parent magma and their mantle sources. A shock-reverberation experiment was also performed on terrestrial orthopyroxenes (opx) to simulate the heavily shocked conditions of ALH 84001 (> 31 GPa [17]).

Peslier, A. H.↗

Computationally Guided Discovery and Experimental Validation of Indole-3-acetic Acid Synthesis Pathways

Elucidating the interaction networks associated with secondary metabolite production in microorganisms is an ongoing challenge made all the more daunting by the rate at which DNA sequencing technology reveals new genes and potential pathways. Developing the culturing methods, expression conditions, and genetic systems needed for validating pathways in newly discovered microorganisms is often not possible. Therefore, new tools and techniques are needed for defining complex metabolic pathways. Here, we describe an in vitro computationally assisted pathway description approach that employs bioinformatic searches of genome databases, protein structural modeling, and protein–ligand-docking simulations to predict the gene products most likely to be involved in a particular secondary metabolite production pathway. This information is then used to direct in vitro reconstructions of the pathway and subsequent confirmation of pathway activity using crude enzyme preparations. As a test system, we elucidated the pathway for biosynthesis of indole-3-acetic acid (IAA) in the plant-associated microbe Pantoea sp. YR343. This organism is capable of metabolizing tryptophan into the plant phytohormone IAA. BLAST analyses identified a likely three-step pathway involving an amino transferase, an indole pyruvate decarboxylase, and a dehydrogenase. However, multiple candidate enzymes were identified at each step, resulting in a large number of potential pathway reconstructions (32 different enzyme combinations). Our approach shows the effectiveness of crude extracts to rapidly elucidate enzymes leading to functional pathways. Furthermore, results are compared to affinity purified enzymes for select combinations and found to yield similar relative activities. Further, in vitro testing of the pathway reconstructions revealed the “underground” nature of IAA metabolism in Pantoea sp. YR343 and the various mechanisms used to produce IAA. Importantly, our experiments illustrate the scalable integration of computational tools and cell-free enzymatic reactions to identify and validate metabolic pathways in a broadly applicable manner.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GL4U: Training the next generation of bioinformaticians, one omics datatype at a time

Spaceflight modifies gene expression in every organism examined to date, including humans. Understanding how these gene expression changes affect physiology is crucial for the development of countermeasures to enable long-duration manned missions. NASA’s GeneLab project provides researchers open access to multi-omics data, including genetic and gene expression data, from spaceflight experiments that can be mined to understand the effects of spaceflight on biological systems. To ensure new knowledge generation through data re-use, it is important to maximize the number of scientists who utilize GeneLab data. Training students on the GeneLab platform is the best way to create long-term adopters of this NASA database and its tools. Turning students into future instructors and advocates will also accelerate the dissemination of these data and tools to the broader scientific community. Therefore, in collaboration with the GeneLab Educational Working Group (EWG), GeneLab has created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab team plans to 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 GeneLab’s space-relevant omics data. During the bootcamp, educators will receive materials and training to enable them to run the bootcamp at their home institutions or alternatively to adapt the content to implement within existing courses, thereby extending the reach of this initiative. The GL4U direct training pilot program was conducted in June 2021 in collaboration with USRA and San Jose State University (SJSU). During the pilot, SJSU students participated in a week-long bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze RNA sequence data. This pilot demonstrates the capacity of GL4U for training young scientists and encouraging data re-use.

Jonathan Matthew Galazka↗

Metal Big Area Additive Manufacturing: Process Modeling and Validation

Metal Big Area Additive Manufacturing (mBAAM) is a new additive manufacturing (AM) technology for printing large-scale 3D objects. mBAAM is based on the gas metal arc welding process and uses a continuous feed of welding wire to manufacture an object. An electric arc forms between the wire and the substrate, which melts the wire and deposits a bead of molten metal along the predetermined path. In general, the welding process parameters and local conditions determine the shape of the deposited bead. The sequence of the bead deposition and the corresponding thermal history of the manufactured object determine the long range effects, such as thermal-induced distortions and residual stresses. Therefore, the resulting performance or final properties of the manufactured object are dependent on its geometry and the deposition path, in addition to depending on the basic welding process parameters. Physical testing is critical for gaining the necessary knowledge for quality prints, but traversing the process parameter space in order to develop an optimized build strategy for each new design is impractical by pure experimental means. Computational modeling and optimization may accelerate development of a build process strategy and saves time and resources. Because computational modeling provides these opportunities, we have developed a physics-based Finite Element Method (FEM) simulation framework and numerical models to support the mBAAM process s development and design. In this paper, we performed a sequentially coupled heat transfer and stress analysis for predicting the final deformation of a small rectangular structure printed using the mild steel welding wire. Using the new simulation technologies, material was progressively added into the FEM simulation as the arc weld traversed the build path. In the sequentially coupled heat transfer and stress analysis, the heat transfer was performed to calculate the temperature evolution, which was used in a stress analysis to evaluate the residual stresses and distortions. In this formulation, we assume that physics is directionally coupled, i.e. the effect of stress of the component on the temperatures is negligible. The experiment instrumentation (measurement types, sensor types, sensor locations, sensor placements, measurement intervals) and the measurements are presented. The temperatures and distortions from the simulations show good correlation with experimental measurements. Ongoing modeling work is also briefly discussed.

Additive Manufacturing↗

Unmanned Aircraft Systems (UAS) Integration in the National Airspace System (NAS) Project: ACAS Xu HITL Overview

This presentation provides an overview of a recently completed human-in-the-loop simulation, conducted as part of the Unmanned Aircraft Systems (UAS) Integration in the National Airspace System (NAS) Project. This study examined how to present resolution advisories (RAs) issued by Airborne Collision Avoidance System (ACAS) Xu, which can be in the vertical dimension, the horizontal dimension, or both (i.e., "blended"). The study varied the location of the ACAS Xu traffic information - it was either presented within an 'integrated' display or a 'standalone' display, where the traffic information was separated from the vehicle control interfaces and navigational information. The presentation covers the test set-up, scenario design, and facilities utilized in this experiment. The primary dependent variables are listed, but no detailed results are included in this outbrief since data analysis is still underway. Goal: assess ACAS Xu Run 5 in a HITL setting to measure pilot & system performance – RWC alerting and guidance – RA alerting and guidance • Horizontal-only, vertical-only, and blended RAs • Strengthening RAs, reversals and added/removed RAs during blended maneuvers – Incorporate realistic sensor noise into the simulation environment – Compare pilot and DAA system performance back to NASA’s Phase 1 DAA MOPS V&V HITL • We leveraged the findings of an engineering analysis conducted in March to help inform how to implement the Xu logic – Part 1 focused on how to display horizontal-only, vertical-only and blended RAs – Part 2 focused on how to display automated RA responses Xu Engineering Analysis Results Part 1 objectives: – Characterize pilot responses to (canned) ACAS Xu RAs in a variety of display configurations • With vs. Without text accompaniment • Simple vs. ‘Advanced’ aural alerting • Results – Pilots struggled to meet 5 seconds initial response requirement • Particularly against horizontal and blended RAs – Pilots failed to respond more quickly to secondary RAs • Expected response time to subsequent RAs = 2.5 seconds No clear effect of the different alerting conditions on response times – Response times primarily driven by RA type • Pilots demonstrated high level of compliance with RAs and self-reported Xu alerting and guidance as being acceptable – 1/5 reported text as being necessary – 4/5 wanted the aural alert to retain the original RA sequence (i.e., issue a follow-on RA second rather than first) – 4/5 wanted to retain the “Maintain Heading/Vertical Speed” aural alert in the event that the pilot reached their target response at the time of secondary RA Based on these results, we decided on the following for the HITL experimental design: – Incorporated an ‘auto-fill’ feature in Vigilant Spirit that removes the need for pilots to manually enter a heading or altitude for RAs • Pilots only have to click ‘Send’ to upload the RA target heading/altitude – Did not include an RA ‘text box’ • The auto-fill feature largely replaces the purpose of the text box – Using a combination of the ‘Basic’ and ‘Advanced’ aural alerting • In case of blended maneuvers will issue “Maintain Heading/Vertical Rate” if pilot has reached 1st RA target at the time the 2nd RA is issued • Integration and testing with Xu Run 5 also resulted in us adding display logic to modify how horizontal RAs are presented – Target heading was shown to update at approx. 1 Hz making it difficult for pilots to implement – Display logic limited horizontal RA strengthening to once every 5 seconds • Did not impact timing of reversals, new RAs (i.e., blended), or CoC Engineering Analysis Results

human systems integration↗

Learning genetic perturbation effects with variational causal inference

Advances in sequencing technologies have enhanced the understanding of gene regulation in cells. In particular, Perturb-seq has enabled high-resolution profiling of the transcriptomic response to genetic perturbations at the single-cell level. This understanding has implications in functional genomics and potentially for identifying therapeutic targets. Various computational models have been developed to predict perturbational effects. While deep learning models excel at interpolating observed perturbational data, they tend to overfit in the lack of enough data and may not generalize well to unseen perturbations. In contrast, mechanistic models, such as linear causal models based on gene regulatory networks, hold greater potential for extrapolation, as they encapsulate regulatory information that can predict responses to unseen perturbations. However, their application has been limited to small studies due to overly simplistic assumptions, making them less effective in handling noisy, large-scale single-cell data. We propose a hybrid approach that combines a mechanistic causal model with variational deep learning, termed Single Cell Causal Variational Autoencoder (SCCVAE). The mechanistic model employs a learned regulatory network to represent perturbational changes as shift interventions that propagate through the learned network. SCCVAE integrates this mechanistic causal model into a variational autoencoder, generating rich, comprehensive transcriptomic responses. Our results indicate that SCCVAE exhibits superior performance over current state-of-the-art baselines for extrapolating to predict unseen perturbational responses. Additionally, for the observed perturbations, the latent space learned by SCCVAE allows for the identification of functional perturbation modules and simulation of single-gene knockdown experiments of varying penetrance, presenting a robust tool for interpreting and interpolating perturbational responses at the single-cell level.

59 BASIC BIOLOGICAL SCIENCES↗

Arbuscular mycorrhizal fungal community responses to drought and nitrogen fertilization in switchgrass stands

Anthropogenic global change is increasing the severity and frequency of abiotic stresses such as drought that are likely to affect soil communities. Arbuscular mycorrhizal fungi (AMF) play important roles in many soil processes, so it is important to understand how drought affects AMF biodiversity. This is especially relevant in agricultural systems where crops rely on AMF associations for water and nutrient uptake, and where management decisions such as crop selection and fertilizer application may influence how the AMF community responds to drought. In this study, we examined the effects of reduced precipitation and nitrogen fertilization on AMF richness, community composition, and root and soil colonization in monocultures of two cultivars of switchgrass (Panicum virgatum) grown for bioenergy feedstock. We conducted a two-year field experiment using rain-out shelters to manipulate precipitation in mature stands of switchgrass growing in a long-term nitrogen fertilization (0 or 56 kg N ha –1 ) experiment at the W.K. Kellogg Biological Station Long-Term Ecological Research site in Michigan, USA. We expected that AMF richness and colonization would decrease due to drought, as predicted by the stress exclusion hypothesis. Contrary to our expectations, we found that drought stress increased AMF species richness in fertilized plots by 15%; there was no effect of drought on AMF richness in unfertilized plots. Drought also significantly altered AMF community composition, primarily due to increases in Rhizophagus taxa abundance, and reduced AMF root colonization in switchgrass by 6%. We also found variation in AMF richness and colonization across switchgrass cultivars as well as sampling dates. Furthermore, the changes in AMF richness and composition that we observed in this study may have implications for perennial bioenergy feedstock selection and management as changes in AMF communities may feedback to affect host plants.

54 ENVIRONMENTAL SCIENCES↗

Aftershocks of a Chemical Explosion in Granite from the Source Physics Experiment Phase I

The Source Physics Experiment (SPE) is a multiphase experiment to better understand explosion source physics and thereby improve explosion monitoring. The rst phase (Phase I) examined the explosion source in a hard-rock medium and took place in a granite outcrop called the Climax Stock section of the Nevada National Security Site (NNSS). This series of chemical explosions are called the Wet Granite Geology (WGG) events, but are usually referred to simply as the SPE events (i.e., SPE-1, SPE-2, etc.). Event information for the chemical explosions is given in Table 1. The study of explosion aftershocks can aid in understanding of in-situ stresses and be used as a discriminant for earthquakes [Ford and Walter, 2010]. Sweeney and Harben reported no observed aftershocks for SPE-1 and -2, respectively. They calculated a minimum magnitude of observation based on the noise oor of the seismic array and predicted at least one or two events in the week after the events using the hard-rock aftershock model from Ford and Labak. Possible explanations for the null observation ranged from instrumental - poor seismometer coupling, to physical - the shallow depth of burial was unable to access the deep tectonic stress that causes some explosion aftershocks. We extend the analysis of Sweeney and Harben to the largest of the SPE Phase I chemical explosions, SPE-5, which was approximately a 5 tonne TNT-equivalent shot at 76.5 m depth. This event registered as an M L 2 on the University of Nevada, Reno seismic network and should produce a measurable aftershock sequence.

58 GEOSCIENCES↗

Enabling Biological Discovery Through Biospecimen Sharing: The Nasa Biological Institutional Scientific Collection

Understanding biological impacts from spaceflight hazards and the subsequent development of countermeasures are a high priority to enable humanity to venture back to the Moon, and then to Mars and beyond. Experiments have been conducted with model organisms flown to space and analogous investigations terrestrially, to identify biological mechanistic impacts from spaceflight hazards and to develop mitigation countermeasures, thus contributing towards basic and applied science goals. However, sending organisms into space is a costly endeavor. To maximize scientific return, all biospecimens not required by spaceflight-relevant Principal Investigators are harvested, preserved, and archived in the NASA Biological Institutional Scientific Collection (NBISC). Biospecimens are collected and preserved according to well-established standard operating procedures to maintain scientific quality and are available on-request by the international scientific community. NBISC currently stores over 32,000 biospecimens from Shuttle, International Space Station, and ground-based space analog investigations. Tissue sharing has resulted in at least 33 publications since 2011 and 51 requests since 2016. Many requests for NBISC biospecimens come from first-time investigators who subsequently submit grants as their point-of-entry into the field of spaceflight biology and health. The NBISC biorepository is part of the NASA ‘Open Science for Life in Space’ collaborative group of projects, which includes NASA Genelab, the Space Biology Program’s Biospecimen Sharing Program, Physical Sciences Informatics, and the Ames Life Sciences Data Archive. NBISC biospecimens have been awarded to NASA Genelab, who then generated various open access science ‘omics datasets through the GeneLab Sample Processing laboratory, with resulting data widely used for biological study. Other NBISC biospecimen awards have led to studies on fecal microbiome analysis, DNA damage analysis using single-cell DNA sequencing, enzymatic-pathway identification involved in spaceflight muscle atrophy, and characterization of ocular morphological changes. Of note, NBISC is expanded to include a new Space Microbial Culture Collection (SMCC) for the collection, identification, documentation, long-term preservation, and distribution of space-related microbial isolates.

Biospecimens↗

The Manufacturing Process for the NASA Composite Crew Module Demonstration Structure

This paper will describe the approaches and methods selected in fabrication of a carbon composite demonstration structure for the Composite Crew Module (CCM) Program. The program is managed by the NASA Safety and Engineering Center with participants from ten NASA Centers and AFRL. Multiple aerospace contractors are participating in the design development, tooling and fabrication effort as well. The goal of the program is to develop an agency wide design team for composite habitable spacecraft. The specific goals for this development project are: a).To gain hands on experience in design, building and testing a composite crew module. b) To validate key assumptions by resolving composite spacecraft design details through fabrication and testing of hardware. This abstract is based on Preliminary Design data..The final design will continue to evolve through the fall of 2007 with fabrication mostly completed by conference date. From a structures perspective, the.CCM can be viewed as a pressure module with variable pressure time histories and a series of both impact and quasi-static, high intensity point, line, and area distributed loads. The portion of the overall space vehicle being designed and. fabricated by the CCM team is just the pressure module and primary loading points. The heaviest point loads are applied and distributed to the pressure module at.an aluminum Service Module/Alternate Launch Abort System (SM/ALAS) fittings and at Main and Drogue Chute fittings. Significant line loads with metal to metal impact is applied at.the Lids ring. These major external point and line loads as well as pressure impact loads (blast and water landing) are applied to the lobed floor though the reentry shield and crushable materials. The pressure module is divided into upper and lower. shells that mate together with a bonded belly band splice joint to create the completed structural assembly. The benefits of a split CCM far outweigh the risks of a joint. These benefits include lower tooling cost and less manufacturing risk. Assembly of the top and bottom halves of the pressure shell will allow access to the interior of the shell throughout remaining fabrication sequence and can also potentially permit extensive installation of equipment and .crew facilities prior to final assembly of the two shell halves. A Pi pre-form is a woven carbon composite material which is provided in pre-impregnated form and frozen for long term storage. The cross-section shape allows the top of the pi to be bonded to a flat or curved surface with a second flat plate composite section bonded between two upstanding legs of the Pi. One of the regions relying on the merits of the Pi pre-form is the backbone. All connections among plates of the backbone structure, including the upper flanges, and to the lobe base of the pressure shell are currently joined by Pi pre-forms. The intersection of backbone composite plates is formed by application of two Pi pre-forms, top flanges and lobed surfaces are bonded with one Pi pre-form. The process of applying the pre-impregnated pi-preform will be demonstrated to include important steps like surface preparation, forming, application of pressure dams, vacuum bagging for consolidation, and curing techniques. Chopped carbon fiber tooling was selected over other traditional metallic and carbon fiber tooling. The requirement of schedule and cost economy for a moderate reuse cure tool warranted composite tooling options. Composite tooling schedule duration of 18 weeks compared favorably against other metallic tooling including invar tooling. Composite tooling also shows significant cost savings over low CTE metallic options. The composite tooling options were divided into two groups and the final decision was based on the cost, schedule, tolerance, temperature, and reuse requirements.

Pelham, Larry↗

Illuminating the pathways to carbon liberation: a systems approach to characterizing the consequential unknowns of carbon transformation and loss from thawing permafrost peatlands (Final Report)

The IsoGenie3 Project delivered new systems-level insights into carbon cycling in thawing permafrost landscapes, with an emphasis on methane and carbon dioxide emissions. From >200 samples from the site collected over a decade, co-analyzed for geochemistry and microbiology, the team recovered ~1,500 assembled microbial genomes and ~1,900 viral population genomes, revealing appreciable genetic novelty - from a new highly abundant bacterial phylum, to novel methane consumers and their activities, to rampant viral novelty. IsoGenie3 linked these organisms to carbon compound transformations (which define the cycling of organic matter in soils, and the loss of the greenhouse gases carbon dioxide and methane), and saw that the microbes at each stage of permafrost thaw had different genetic potential to degrade categories of compounds, expressed that genetic potential differently, and actually transformed carbon compounds into greenhouse gases in different ways. IsoGenie 3 identified that some of the thaw-stage differences were due to plant-microbiome relationships; the plant species across the thaw gradient contributed different carbon compounds into the soil, and hosted distinct microbiota (differing among parts of plants as well as species). Lastly, microbes in the saturated post-thaw conditions appeared likely to contribute to the mobilization and toxification of mercury released during thaw. In parallel with ongoing field sampling and analysis, hypotheses arising from field observations were tested via lab incubation experiments. When communities are taken out of their native habitats, they behave differently, and the team first rigorously quantified the magnitude of this effect on microbiome composition and functional capacity, organic matter composition, and gas production; overall the main system processes were maintained in the lab incubations under the conditions tested. Further, the microbial data could inform geochemical reaction network models of those processes. Then, the team ran experiments with additions of compounds, varying temperature, and “live” vs. “dead” peat (the latter having been gamma irradiated, with a few additional variants to control for methodological artifacts). From these, we (a) determined the importance of plant-derived soluble phenolic compounds in bogs’ extraordinary recalcitrance of organic matter, and carbon gas emissions skewed to carbon dioxide; (b) proposed an abiotic ‘tanning’ mechanism, which could contribute to Sphagnum’s inhibitory effect on anaerobic decomposition through alteration of N availability. IsoGenie3 illuminated longer-term and landscape-scale interactions of permafrost thaw and carbon cycling, advancing knowledge of the drivers of methane dynamics not only across in the permafrost-associated peatland (where hydrology and plant communities dictate microbiomes) but also their interconnected lakes (where sediment carbon quality and resident microbiota are determined by position within lake, and lake features). By leveraging observations of site methane dynamics extending well before this project, the team was able to construct a 44-year portrait of the interplay of permafrost thaw, hydrology, vegetation dynamics, and carbon gas emissions, and the doubling of the fully-thawed fens over this time. From the detailed study of this focal site, IsoGenie3 also aimed to improve model representation of these kinds of sites and processes. To improve predictions of methane transformations, we incorporated acetate and isotope dynamics into the ‘DNDC’ biogeochemistry model. In addition, recovered genomes were grouped into ‘functional groups’, i.e. the genomes that perform a specific function of interest, then used to parameterize maximum growth rate and optimum growth temperature (via signatures in their sequence composition) for the BioCrunch model. The BioCrunch model was then in turn used to test the impact of increasing functional resolution of the microbes, on the carbon gas emissions. Lastly for modeling, the ecosys model was parameterized from the microbial and other data, and used to evaluate drivers of e.g. change in methane emissions. Finally, this project also led to the development of a range of new methods and tools, a new metric of organic matter decomposability, as well as a graph-database solution to multidisciplinary data storage and querying. This project’s ongoing analyses at our focal site also contributed to broader advancements in understanding elements of genetic plasticity and methane metabolism, climate change microbiology and community assembly, global peatland geochemistry and Arctic lakes’ roles in climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗

How Solvent Mediates the Catalytic Fate of 2-Methoxyphenol in Hydrodeoxygenation Catalysis?

Kinetic and isotopic assessments combined with theoretical calculations shed light on the mechanistic differences in terms of the number of hydrogen addition steps and the electronic charges of reactive hydrogen in the catalytic sequence leading to the Ar−OCH 3 scission of 2-methoxyphenol occurring at various interfaces of vapor−Ru, cyclohexane−Ru, and water−Ru. At vapor−Ru and cyclohexane−Ru interfaces, the initial hydrogen adatom (H*) additions on the phenyl ring disrupt its aromaticity, as a step required to occur before kinetically relevant Ar−OCH 3 scission on an ensemble of Ru sites. The number of H* addition events prerequisite to the formation of the kinetically relevant Ar−OCH 3 scission transition state, however, is larger at the cyclohexane−Ru interface than those at the vapor−Ru and water−Ru interfaces. The preferential solvation of 2-methoxyphenol derived reaction precursors and H* weakens their adsorption on Ru sites, which leads to a decrease in the activation barrier for the third H* addition step and in turn a larger number of H* additions. At the water−Ru interface, water as a polar protic solvent promotes the Ar−OCH 3 scission by enabling a mechanistically distinct catalytic route an adjacent water molecule from the solvent layer assists with the intramolecular proton shuttling from the hydroxyl group (−OH) to the vicinal methoxy group (−OCH 3 ) of 2-methoxyphenol, evolving a highly charged transition state that is further stabilized by the water solvent layer, thereby leading to Ar−OCH 3 scission rate constants that are much higher than those at the vapor−Ru interface and, when comparing at the same H 2 chemical potential, higher Ar−OCH 3 scission turnovers. Furthermore, these distinct mechanistic details of the Ar−OCH 3 scission at various reaction interfaces, inferred from experiment and theory, illustrate how a solvent either solvates reaction intermediates and transition states or directly participates in the formation of kinetically relevant transition states, leading to changes in the free energy landscape, thus rewriting the catalytic fates in hydrodeoxygenation reactions.

09 BIOMASS FUELS↗

Distribution of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria in hot spring microbial mats

Oligodeoxynucleotide hybridization probes were developed to complement specific regions of the small subunit (SSU) rRNA sequences of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria, which inhabit hot spring microbial mats. The probes were used to investigate the natural distribution of SSU rRNAs from these species in mats of Yellowstone hot springs of different temperatures and pHs as well as changes in SSU rRNA distribution resulting from 1-week in situ shifts in temperature, pH, and light intensity. Synechococcus lividus Y-7c-s SSU rRNA was detected only in the mat of a slightly acid spring, from which it may have been initially isolated, or when samples from a more alkaline spring were incubated in the more acid spring. Chloroflexus aurantiacus Y-400-fl SSU rRNA was detected only in a high-temperature mat sample from the alkaline Octopus Spring or when lower-temperature samples from this mat were incubated at the high-temperature site. SSU rRNAs of uncultivated species were more widely distributed. Temperature distributions and responses to in situ temperature shifts suggested that some of the uncultivated cyanobacteria might be adapted to high-, moderate-, and low-temperature ranges whereas an uncultivated Chloroflexus-like bacterium appears to have broad temperature tolerance. SSU rRNAs of all uncultivated species inhabiting a 48 to 51 degrees C Octopus Spring mat site were most abundant in the upper 1 mm and were not detected below a 2.5-to 3.5-mm depth, a finding consistent with their possible phototrophic nature. However, the effects of light intensity reduction on these SSU rRNAs were variable, indicating the difficulty of demonstrating a phototrophic phenotype in light reduction experiments.

Non-NASA Center↗

Investigation of the Glen Torridon Clay-Bearing Unit and Overlying Greenheugh Pediment by the Sample Analysis at Mars Instrument Suite

Exploring the Glen Torridon (GT) clay-bearing unit in Gale crater has long been a prime goal for the Mars Science Laboratory (MSL) because of spectral signatures of smectite identified from orbit. Smectite clay minerals can indicate habitable environments [1,2] and possibly facilitate the preservation of organic compounds [e.g., 3-7].Also, sulfate-bearing layers overlie GT and this sequence may record a large-scale change in aqueous conditions overtime [8].The Sample Analysis at Mars (SAM) instrument suitehas been essential in understanding volatile-bearing phases in Gale crater materials. SAM EGA has detected H2O, CO2, O2, H2, SO2, H2S, HCl, NO, and other trace gases, including organic fragments, evolved from many samples on heating. The identity and evolution temperature of evolved gases can support mineral detection by CheMin instrument X-ray diffraction (XRD)and place constraints on trace volatile-bearing phases, clay mineral compositions, and X-ray amorphous materials. In GT, SAM analyzed the sample Kilmarie (KM) from the Jura member, Glen Etive (GE), Mary Anning (MA) and Groken (GR)from the Knockfarril Hill member (KHm), Glasgow (GG) and Hutton (HU) from the fractured Intermediate Unit (fIU), and Edinburgh (EB) from the Stimson formation rocks of the Greenheugh Pediment (GP). The Jura, KHm and fIU are all members of the Murray formation. HU was sampled near the basal Siccar Point group (SPg) unconformity between the fIU and GP, in an area that exhibits a brighter tone and differences in geochemistry compared to Murray materials down-section [9,10]. CheMin XRD of most samples (except for HU and EB)showed large abundances of smectite clay minerals (~25-35%) and all samples showed X-ray amorphous materials and relatively low amounts of well-crystalline hematite[11]. SAM evaluated mineralogy through evolved gas analysis mass spectrometry (EGA) while detailed organic chemistry of several samples was examined by pyrolysis gas chromatography mass spectrometry and wet chemistry experiments [12,13].Here we discuss data and interpretations from SAM EGA analyses.

Mars↗

NASA Tech Briefs, September 2013

Topics include: ISS Ammonia Leak Detection Through X-Ray Fluorescence; A System for Measuring the Sway of the Vehicle Assembly Building; Fast, High-Precision Readout Circuit for Detector Arrays; Victim Simulator for Victim Detection Radar; Hydrometeor Size Distribution Measurements by Imaging the Attenuation of a Laser Spot; Quasi-Linear Circuit; High-Speed, High-Resolution Time-to-Digital Conversion; Li-Ion Battery and Supercapacitor Hybrid Design for Long Extravehicular Activities; Ultrasonic Low-Friction Containment Plate for Thermal and Ultrasonic Stir Weld Processes; High-Powered, Ultrasonically Assisted Thermal Stir Welding; Next-Generation MKIII Lightweight HUT/Hatch Assembly; Centrifugal Sieve for Gravity-Level-Independent Size; Segregation of Granular Materials; Ion Exchange Technology Development in Support of the Urine Processor Assembly; Nickel-Graphite Composite Compliant Interface and/or Hot Shoe Material; UltraSail CubeSat Solar Sail Flight Experiment; Mechanism for Deploying a Long, Thin-Film Antenna From a Rover; Counterflow Regolith Heat Exchanger; Acquisition and Retaining Granular Samples via a Rotating Coring Bit; Very-Low-Cost, Rugged Vacuum System; Medicine Delivery Device With Integrated Sterilization and Detection; FRET-Aptamer Assays for Bone Marker Assessment, C-Telopeptide, Creatinine, and Vitamin D; Multimode Directional Coupler for Utilization of Harmonic Frequencies from TWTAs; Dual-Polarization, Multi-Frequency Antenna Array for use with Hurricane Imaging Radiometer; Complementary Barrier Infrared Detector (CBIRD) Contact Methods; Autonomous Control of Space Nuclear Reactors; High-Power, High-Speed Electro-Optic Pockels Cell Modulator; Covariance Analysis Tool (G-CAT) for Computing Ascent, Descent, and Landing Errors; Enigma Version 12; Micrometeoroid and Orbital Debris (MMOD) Shield Ballistic Limit Analysis Program; Spitzer Telemetry Processing System; Planetary Protection Bioburden Analysis Program; Wing Leading Edge RCC Rapid Response Damage Prediction Tool (IMPACT2); ISSM: Ice Sheet System Model; Automated Loads Analysis System (ATLAS); Integrated Main Propulsion System Performance Reconstruction Process/Models. Phoenix Telemetry Processor; Contact Graph Routing Enhancements Developed in ION for DTN; GFEChutes Lo-Fi; Advanced Strategic and Tactical Relay Request Management for the Mars Relay Operations Service; Software for Generating Troposphere Corrections for InSAR Using GPS and Weather Model Data; Ionospheric Specifications for SAR Interferometry (ISSI); Implementation of a Wavefront-Sensing Algorithm; Sally Ride EarthKAM - Automated Image Geo-Referencing Using Google Earth Web Plug-In; Trade Space Specification Tool (TSST) for Rapid Mission Architecture (Version 1.2); Acoustic Emission Analysis Applet (AEAA) Software; Memory-Efficient Onboard Rock Segmentation; Advanced Multimission Operations System (ATMO); Robot Sequencing and Visualization Program (RSVP); Automating Hyperspectral Data for Rapid Response in Volcanic Emergencies; Raster-Based Approach to Solar Pressure Modeling; Space Images for NASA JPL Android Version; Kinect Engineering with Learning (KEWL); Spacecraft 3D Augmented Reality Mobile App; MPST Software: grl_pef_check; Real-Time Multimission Event Notification System for Mars Relay; SIM_EXPLORE: Software for Directed Exploration of Complex Systems; Mobile Timekeeping Application Built on Reverse-Engineered JPL Infrastructure; Advanced Query and Data Mining Capabilities for MaROS; Jettison Engineering Trajectory Tool; MPST Software: grl_suppdoc; PredGuid+A: Orion Entry Guidance Modified for Aerocapture; Planning Coverage Campaigns for Mission Design and Analysis: CLASP for DESDynl; and Space Place Prime.

Source record↗

Methyl formate oxidation kinetics up to 100 atm

Methyl formate (MF, CH3OCHO), the simplest ester, is a representative oxygenated fuel with high oxygen content, and low sooting tendency. However, its oxidation behavior under high-pressure and intermediate-temperature conditions remains insufficiently understood, especially where low-temperature peroxy radical chemistry, methanol chemistry, and pressure-dependent reaction pathways play a critical role. In this study, MF oxidation experiments were conducted in the Princeton supercritical-pressure jet-stirred reactor (SP-JSR) at 20 and 100 atm over the temperature range of 400–950 K under both fuel-lean and fuel-rich conditions. Based on the experimental results, an updated HP-Mech was developed by incorporating previous MF sub-mechanisms, expanded low-temperature peroxy pathways, and evaluated pressure-dependent decomposition kinetics. The newly updated HP-Mech shows greatly improved performance in predicting the onset temperature, the key intermediate species fractions, methanol formation, and the progression of MF oxidation across all the experimental conditions. Path flux analysis indicates that MF consumption at the onset stage is dominated by H-abstraction at the methyl site, forming CH2OCHO radicals that lead to the formation and isomerization of O2CH2OCHO, driving low-temperature chain propagation. Moreover, H-abstraction at the formate site forms CH3OCO radicals that preferentially decompose to CH3, initiating the methanol formation pathway linked to CH3O2 and HO2 chemistry. At the same time, HO2 formation is strongly coupled to MF oxidation through multiple MF-derived radical pathways. HCO originates from MF oxidation and acts as a key coupling species linking fuel consumption to HO2 buildup, especially under high-pressure and intermediate-temperature conditions. In addition to this dominant channel, supplementary HO2 formation pathways involving CH3, CH3O, CH2OH, and CH3O2 reacting with O2 further connect methanol chemistry and oxygenated radical chemistry to the HO2 pool, indicating the central role of HO2 in governing MF oxidation. Sensitivity analysis identifies MF with OH/HO2/CH3O2 reactions and the HO2/H2O2/OH sequence as the key factors controlling reactivity in the high-pressure and intermediate-temperature regime. MF directly reacts with OH/HO2/CH3O2 to consume the fuel and produce reactive radicals like CH2OCHO and CH3OCO that undergo subsequent oxidation pathways. Moreover, HO2 recombination suppresses oxidation at lower temperatures, while thermal decomposition of H2O2 accelerates OH production and promotes fuel consumption as temperature increases. The direct formation of active OH from HO2 radicals further completes the mechanism, improving its prediction especially during the oxidation onset stage.

Low-temperature Chemistry↗