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DOE OSTI2022

Magnitude-squared Coherence: A Powerful Tool for Disentangling Doppler Planet Discoveries from Stellar Activity

Abstract If Doppler searches for Earth-mass, habitable planets are to succeed, observers must be able to identify and model out stellar activity signals. Here we demonstrate how to diagnose activity signals by calculating the magnitude-squared coherence C ˆ xy 2 ( f ) between an activity-indicator time series x t and the radial-velocity (RV) time series y t . Since planets only cause modulation in RV, not in activity indicators, a high value of C ˆ xy 2 ( f ) indicates that the signal at frequency f has a stellar origin. We use Welch’s method to measure coherence between activity indicators and RVs in archival observations of GJ 581, α Cen B, and GJ 3998. High RV-H α coherence at the frequency of GJ 3998 b and high RV-S index coherence at the frequency of GJ 3998c, indicate that the planets may actually be stellar signals. We also replicate previous results showing that GJ 581 d and g are rotation harmonics and demonstrate that α Cen B has activity signals that are not associated with rotation. Welch’s power spectrum estimates have cleaner spectral windows than Lomb–Scargle periodograms, improving our ability to estimate rotation periods. We find that the rotation period of GJ 581 is 132 days, with no evidence of differential rotation. Welch’s method may yield unacceptably large bias for data sets with N < 75 observations and works best on data sets with N > 100. Tapering the time-domain data can reduce the bias of the Welch’s power spectrum estimator, but observers should not apply tapers to data sets with extremely uneven observing cadence. A software package for calculating magnitude-squared coherence and Welch’s power spectrum estimates is available on github.

Dodson-Robinson, Sarah E. (ORCID:0000000287964974)↗

NASA NTRS1986

Cooperation of catalysts and templates

In order to understand how self-reproducing molecules could have originated on the primitive Earth or extraterrestrial bodies, it would be useful to find laboratory models of simple molecules which are able to carry out processes of catalysis and templating. Furthermore, it may be anticipated that systems in which several components are acting cooperatively to catalyze each other's synthesis will have different behavior with respect to natural selection than those of purely replicating systems. As the major focus of this work, laboratory models are devised to study the influence of short peptide catalysts on template reactions which produce oligonucleotides or additional peptides. Such catalysts could have been the earliest protoenzymes of selective advantage produced by replicating oligonucleotides. Since this is a complex problem, simpler systems are also studied which embody only one aspect at a time, such as peptide formation with and without a template, peptide catalysis of nontemplated peptide synthesis, and model reactions for replication of the type pioneered by Orgel.

White, D. H.↗

NASA NTRS1998

RNA Research

It is generally believed that an RNA World existed at an early stage in the history of life. During this early period, RNA molecules are seen to be potentially involved in both catalysis and the storage of genetic information. It is widely believed that this RNA World was extensive and therefore a sophisticated nucleic acid replication machinery would presumably predate the translation machinery which would not be needed until later stages in the development of life. This view of an extended RNA World is not necessarily correct. From the point of view of exobiology, the difference in these two views mainly affects the significance of studies of the extent of catalysis possible by RNA- In either case, the origin of the translation machinery and the principles of RNA evolution remain central problems in exobiology. Translation presents several interrelated themes of inquiry for exobiology. First, it is essential, for understanding the very origin of life, how peptides and eventually proteins might have come to be made on the early Earth in a template directed manner. Second, it is necessary to understand how a machinery of similar complexity to that found in the ribosomes of modem organisms came to exist by the time of the last common ancestor (as detected by 16S RRNA sequence studies). Third, the RNAs that comprise the ribosome are themselves likely of very early origin and studies of their history may be very informative about the nature of the RNA World. Moreover, studies of these RNAs will contribute to a better understanding of the potential roles of RNA in early evolution.

Source record↗

DOE OSTI2020

Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities

In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting that multiple functional guilds feed on methane, likely through guild-to-guild carbon transfer, and potentially through intraguild and intraspecies interactions. We observed that, under two simulated dioxygen partial pressures—low versus high—community trajectories were different, with considerable variability among the replicates. In all microcosms, four major functional guilds were prominently present, representing Methylococcaceae (the true methanotrophs), Methylophilaceae (the nonmethanotrophic methylotrophs), Burkholderiales, and Bacteroidetes. Additional functional guilds were detected in multiple samples, such as members of Opitutae, as well as the predatory species, suggesting additional complexity for methane-oxidizing communities. Metatranscriptomic analysis suggested simultaneous expression of the two alternative types of methanol dehydrogenases in both Methylococcaceae and Methylophilaceae, while high expression of the oxidative/nitrosative stress response genes suggested competition for dioxygen among the community members. The transcriptomic analysis further suggested that Burkholderiales likely feed on acetate that is produced by Methylococcaceae under hypoxic conditions, while Bacteroidetes likely feed on biopolymers produced by both Methylococcaceae and Methylophilaceae.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1999

IRIS Mariner 9 Data Revisited: An Instrumental Effect - 1

Small spurious features are present in data from the Mariner 9 Infrared Interferometer Spectrometer (IRIS). These represent a low amplitude replication of the spectrum with a doubled wavenumber scale. This replication arises principally from an internal reflection of the interferogram at the input window. An algorithm is provided to correct for the effect, which is at the 2% level. We believe that the small error in the uncorrected spectra does not materially affect previous results; however, it may be significant for some future studies at short wavelengths. The IRIS spectra are also affected by a coding error in the original calibration that results in only positive radiances. This reduces the effectiveness of averaging spectra to improve the signal to noise ratio at small signal levels.

Formisano, V.↗

DOE OSTI2024

Implementation of Detailed Polyethylene Pyrolysis Kinetics into CFD Simulations using Machine Learning

Municipal solid waste (MSW) and waste plastics have received significant attention due to the issues of waste generation and storage, as well as their potential as an energy resource. High-density polyethylene (HDPE) makes up a large portion of plastic waste and has been the subject of several conversion studies. However, the mechanisms associated with converting HDPE through pyrolysis and gasification are extensive and complex making them difficult to implement into high-fidelity computational fluid dynamic (CFD) simulations. For this project, a primary pyrolysis mechanism containing 42 unique species and 737 heterogeneous reactions was used to generate kinetic data over a range of operating conditions. A machine learning (ML) model was developed to replicate the results of the detailed pyrolysis mechanism while significantly increasing the computational efficiency. A deep operator network (DeepONet) architecture was adopted to train the model using time steps relevant to CFD simulations. The ML used physics-based loss functions to ensure mass conservation. The ML model has been deployed in simple MFiX CFD simulations, single particle, and an experimental drop tube reactor, and has shown promising performance compared to the original scheme.

Houston, Ross↗

NASA NTRS2001

A Structural and Molecular Approach for the Study Biomarkers

Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life, is referred to as organic synthesis on mineral surfaces. Furthermore, it is suggested that the interaction between mineral surfaces and simple organic molecules resulted in the formation of amino acids, RNA, and perhaps other more complex molecules such as proteins. On the other hand, in natural systems, it is recognized that functional groups on cell walls or membranes of microorganisms serve as sites of nucleation and crystallization. The precise replication of biominerals with controlled structure, morphology, size and texture is not confined to higher organisms as it also occurs in primitive prokaryotic cells such as magnetotactic bacteria and cyanobacteria. This suggests that the principal strategies of biomineralization were established early on in the evolutionary history of organisms. It is critical, therefore, to search for common mechanisms within diverse biological systems. One such common factor is the capability for organization and self-assembly. Organic macromolecules such as proteins and lipids can aggregate and polymerize forming membranes or extracellular matrix. At the organic-inorganic interface, several factors such as lattice geometry, polarity, stereochemistry and topography may act in concert to control nucleation and growth of crystals. Although several models have been proposed that discuss the significance of these factors for biomineralization, no comprehensive experimental data are available. In contrast to crystallization in exclusively inorganic systems, the kinetics of reaction and structural relationships between organic and inorganic phases in biominerals or biomimetic material is poorly understood. For example, it is not clear if the concept of epitactic growth (geometrical matching of unit cells at the interface of a secondary crystal growing on a primary crystal) applies to organic-inorganic systems. In contrast to inorganic templates that often have a smooth and rigid surface that promotes epitactic growth, biological substrates are usually rough and result in a large degree of mismatch. It is apparent that factors controlling the reaction at the crystal-matrix interface are strongly dependent upon the nature of the substrate. Therefore, characterization of the assembled organic surface and surface structure of the inorganic phase is crucial to understanding the processes of biomineralization. The focus of our research is the investigation of the processes leading to the nucleation and growth of crystals on both natural and synthetic systems through an interdisciplinary approach that integrates molecular biology, morphology and mineralogy using advanced preparation and analytical techniques. We have studied run-products, particularly magnetite, siderite and other carbonates, that resulted from extracellular biomineralization by extremophiles isolated from a variety of extreme environments ranging from permafrost to hydrothermal vent systems. The results of this study are critical to recognizing biomarkers in terrestrial and extraterrestrial environments.

Thomas-Keprta, Kathie↗

DOE OSTI2023

Improving Experimental Design through Uncertainty Analysis

In this paper, the development of a fission-gas collecting and physical-analysis-enabling instrument was proposed for small-volume determination. Analysis specifications require a design capable of accurately and repeatably determining volumes in the range of 0.07–2.5 mL. This system relies on a series of gas expansions originating from a cylinder with known internal volume. The combined gas law is used to derive the unknown volumes from these expansions. Initial system designs included one of two known volumes, 11.85 ± 0.34 mL and 5.807 ± 0.078 mL, with a manifold volume of 32 mL. Results obtained from modeling this system’s operation showed that 0.07 mL can be determined with a relative expanded uncertainty greater than 300% (k = 2) for a single replicate, which was unacceptable for the proposed experimental design. Initial modeling showed that the volume connecting the known volume and rodlet, i.e., the manifold volume, and the sensitivity of the pressure sensor were key contributors to the expanded uncertainty of the measured rodlet volume. The system’s design limited the available options for pressure sensors, so emphasis was placed on the design of the manifold volume. The final system design reduced the manifold volume to 17 mL. These changes in design, combined with replicate analysis, were able to reduce the relative expanded uncertainty by ±12% (k = 2) for the 0.07 mL volume.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Revisiting the activity of two poly(vinyl chloride)- and polyethylene-degrading enzymes

Biocatalytic degradation of non-hydrolyzable plastics is a rapidly growing field of research, driven by the global accumulation of waste. Enzymes capable of cleaving the carbon-carbon bonds in synthetic polymers are highly sought-after as they may provide tools for environmentally friendly plastic recycling. Despite some reports of oxidative enzymes acting on non-hydrolyzable plastics, including polyethylene or poly(vinyl chloride), the notion that these materials are susceptible to efficient enzymatic degradation remains controversial, partly driven by a general lack of studies independently reproducing previous observations. Here, we attempt to replicate two recent studies reporting that deconstruction of polyethylene and poly(vinyl chloride) can be achieved using an insect hexamerin from Galleria mellonella (so-called “Ceres”) or a bacterial catalase-peroxidase from Klebsiella sp., respectively. Reproducing previously described experiments, we do not observe any activity on plastics using multiple reaction conditions and multiple substrate types. Digging deeper into the discrepancies between the previous data and our observations, we show how and why the original experimental results may have been misinterpreted.

36 MATERIALS SCIENCE↗

NASA NTRS2010

Automated, Miniaturized Instrument for Measuring Gene Expression in Space

To facilitate astrobiological studies on the survival and adaptation of microorganisms and mixed microbial cultures to space environment, we have been developing a fully automated, miniaturized system for measuring their gene expression on small spacecraft. This low-cost, multi-purpose instrument represents a major scientific and technological advancement in our ability to study the impact of the space environment on biological systems by providing data on cellular metabolism and regulation orders of magnitude richer than what is currently available. The system supports growth of the organism, lyse it to release the expressed RNA, label the RNA, read the expression levels of a large number of genes by microarray analysis of labeled RNA and transmit the measurements to Earth. To measure gene expression we use microarray technology developed by CombiMatrix, which is based on electrochemical reactions on arrays of electrodes on a semiconductor substrate. Since the electrical integrity of the microarray remains intact after probe synthesis, the circuitry can be employed to sense nucleic acid binding at each electrode. CombiMatrix arrays can be sectored to allow multiple samples per chip. In addition, a single array can be used for several assays. The array has been integrated into an automated microfluidic cartridge that uses flexible reagent blisters and pinch pumping to move liquid reagents between chambers. The proposed instrument will help to understand adaptation of terrestrial life to conditions beyond the planet of origin, identify deleterious effects of the space environment, develop effective countermeasures against these effects, and test our ability to sustain and grow in space organisms that can be used for life support and in situ resource utilization during long-duration space exploration. The instrument is suitable for small satellite platforms, which provide frequent, low cost access to space. It can be also used on any other platform in space, including the ISS. It can be replicated and used with only small modifications in multiple biological experiments with a broad range of goals in mind.

Pohorille, A.↗

DOE OSTI2023

Nitrogen addition alters soil fungal communities, but root fungal communities are resistant to change

Plants are colonized by numerous microorganisms serving important symbiotic functions that are vital to plant growth and success. Understanding and harnessing these interactions will be useful in both managed and natural ecosystems faced with global change, but it is still unclear how variation in environmental conditions and soils influence the trajectory of these interactions. In this study, we examine how nitrogen addition alters plant-fungal interactions within two species of Populus - Populus deltoides and P. trichocarpa. In this experiment, we manipulated plant host, starting soil (native vs. away for each tree species), and nitrogen addition in a fully factorial replicated design. After ~10 weeks of growth, we destructively harvested the plants and characterized plant growth factors and the soil and root endosphere fungal communities using targeted amplicon sequencing of the ITS2 gene region. Overall, we found nitrogen addition altered plant growth factors, e.g., plant height, chlorophyll density, and plant N content. Interestingly, nitrogen addition resulted in a lower fungal alpha diversity in soils but not plant roots. Further, there was an interactive effect of tree species, soil origin, and nitrogen addition on soil fungal community composition. Starting soils collected from Oregon and West Virginia were dominated by the ectomycorrhizal fungi Inocybe (55.8% relative abundance), but interestingly when P. deltoides was grown in its native West Virginia soil, the roots selected for a high abundance of the arbuscular mycorrhizal fungi, Rhizophagus. These results highlight the importance of soil origin and plant species on establishing plant-fungal interactions.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2006

Chance of Necessity: Modeling Origins of Life

The fundamental nature of processes that led to the emergence of life has been a subject of long-standing debate. One view holds that the origin of life is an event governed by chance, and the result of so many random events is unpredictable. This view was eloquently expressed by Jacques Monod in his book Chance or Necessity. In an alternative view, the origin of life is considered a deterministic event. Its details need not be deterministic in every respect, but the overall behavior is predictable. A corollary to the deterministic view is that the emergence of life must have been determined primarily by universal chemistry and biochemistry rather than by subtle details of environmental conditions. In my lecture I will explore two different paradigms for the emergence of life and discuss their implications for predictability and universality of life-forming processes. The dominant approach is that the origin of life was guided by information stored in nucleic acids (the RNA World hypothesis). In this view, selection of improved combinations of nucleic acids obtained through random mutations drove evolution of biological systems from their conception. An alternative hypothesis states that the formation of protocellular metabolism was driven by non-genomic processes. Even though these processes were highly stochastic the outcome was largely deterministic, strongly constrained by laws of chemistry. I will argue that self-replication of macromolecules was not required at the early stages of evolution; the reproduction of cellular functions alone was sufficient for self-maintenance of protocells. In fact, the precise transfer of information between successive generations of the earliest protocells was unnecessary and could have impeded the discovery of cellular metabolism. I will also show that such concepts as speciation and fitness to the environment, developed in the context of genomic evolution also hold in the absence of a genome.

Pohorille, Andrew↗

NASA NTRS2003

The Chemistry of Early Self-Replicating Systems

The NASA Specialized Center of Research and Training in Exobiology (NSCORT/Exobiology) is a program within the UCSD California Space Institute (Dr. Wolfgang Berger, Director) currently funded by a second 5 year Federal Demonstration Project Grant from NASA. Its specific aims are: 1. The support and training of Postdoctoral, Graduate, and Undergraduate Fellows in Exobiology. 2. The support of research by the Principal Investigators and Fellows in the field of Exobiology. 3. Outreach programs emphasizing the dissemination and exchange of information concerning Exobiology within the scientific community, primary, secondary and college students, and the general public. 4. Host of the 1999 meeting of the International Society for the Study of the Origin of Life (ISSOL) held at the University of California, San Diego in La Jolla, California, from Sunday, July 11 through Friday, July 16,1999.

Bada, Jeffrey L.↗

DOE OSTI2024

Investigation of the cesium activation of Ga⁢N photocathodes by low-energy electron microscopy

Low-energy electron microscopy (LEEM) was performed on p-Ga⁢N samples during in situ cesium deposition. LEEM images of electron reflectivity recorded as a function of the incident electron energy at different Cs coverages allowed to spatially resolve the evolution of the local work function (WF) during the activation process. While the average WF drops by more than 3 eV, the local WF remains quite uniform across the surface throughout the activation process. Maximum fluctuations of less than 0.2 eV were observed in the WF maps for Cs coverage of a fraction of a monolayer. These fluctuations are mainly related to the surface topography, in particular, to the atomic steps’ structure, which replicates the substrate miscut. Apart from these weak spatial fluctuations, no Cs clusters that would induce strong local WF contrast were observed at the scale of the 20-nm resolution of the measurements. These observations agree with the simple model of semiconductor activation to negative electron affinity that describes the formation of a dipole layer as responsible for the lowering of the WF. Additionally, at complete Cs coverage, the WF becomes fully homogeneous over the surface, smoothing out features originating from defects and topography.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS2000

Self-organizing biochemical cycles

I examine the plausibility of theories that postulate the development of complex chemical organization without requiring the replication of genetic polymers such as RNA. One conclusion is that theories that involve the organization of complex, small-molecule metabolic cycles such as the reductive citric acid cycle on mineral surfaces make unreasonable assumptions about the catalytic properties of minerals and the ability of minerals to organize sequences of disparate reactions. Another conclusion is that data in the Beilstein Handbook of Organic Chemistry that have been claimed to support the hypothesis that the reductive citric acid cycle originated as a self-organized cycle can more plausibly be interpreted in a different way.

NASA Discipline Exobiology↗

NASA NTRS2005

VERSE - Virtual Equivalent Real-time Simulation

Distributed real-time simulations provide important timing validation and hardware in the- loop results for the spacecraft flight software development cycle. Occasionally, the need for higher fidelity modeling and more comprehensive debugging capabilities - combined with a limited amount of computational resources - calls for a non real-time simulation environment that mimics the real-time environment. By creating a non real-time environment that accommodates simulations and flight software designed for a multi-CPU real-time system, we can save development time, cut mission costs, and reduce the likelihood of errors. This paper presents such a solution: Virtual Equivalent Real-time Simulation Environment (VERSE). VERSE turns the real-time operating system RTAI (Real-time Application Interface) into an event driven simulator that runs in virtual real time. Designed to keep the original RTAI architecture as intact as possible, and therefore inheriting RTAI's many capabilities, VERSE was implemented with remarkably little change to the RTAI source code. This small footprint together with use of the same API allows users to easily run the same application in both real-time and virtual time environments. VERSE has been used to build a workstation testbed for NASA's Space Interferometry Mission (SIM PlanetQuest) instrument flight software. With its flexible simulation controls and inexpensive setup and replication costs, VERSE will become an invaluable tool in future mission development.

virtual real time↗

NASA NTRSDate not supplied

Performance of the 12.5-kW Advanced Electric Propulsion System Engineering Test Unit Hall Thruster

This work presents a summary of the performance test campaign of the 12.5 kW Advanced Electric Propulsion System (AEPS) Engineering Test Unit 2 (ETU-2) thruster produced by Aerojet Rocketdyne. This test campaign had three major goals: to assess design compliance with thruster requirements, provide a comparison to the previously-tested NASA Hall Effect Rocket with Magnet Shielding (HERMeS) Technology Demonstration Units (TDUs) from which the AEPS ETU design was derived, and support AEPS application on the Power and Propulsion Element (PPE). Assessments of ETU-2 performance were conducted at discharge powers of 2.6 to 13.1 kW, which encompasses the original AEPS throttle conditions as well as those most relevant for AEPS application on PPE. The results from the test campaign indicate that ETU-2 performance meets or exceeds all AEPS thruster performance requirements and matches the values and trends previously measured with the HERMeS TDUs. In addition, similar to the HERMeS TDUs, ETU-2 performance showed minimal variation over approximately 1636 h of operating time due to the incorporation of magnetic shielding. Taken together, these results show that the AEPS design is successfully replicating the performance of the HERMeS TDUs to within the empirical uncertainty and meeting its performance requirements as the design progresses to its Critical Design Review.

HERMeS↗

NASA NTRSDate not supplied

Performance of the 12.5-kW Advanced Electric Propulsion System Engineering Test Unit Hall Thruster

Jason D Frieman↗