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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
NASA NTRS1985

Planning for VRM: Radar and sonar studies of volcanic terrains on Earth, Venus and Mars

Venera 15 and 16 radar images of Venus, together with Earth based data from the Arecibo Observatory, indicate that volcanism has played an important role in the evolution of the Venusian landscape. At the end of this decade, NASA's Venus Radar Mapper (VRM) spacecraft will return near global information that will further constrain the planet's geologic history. Due to the diversity of volcano/tectonic features that have already been identified on Venus, and the intrinsic differences between radar images and conventional photography, additional expertise is being developed with which to interpret the VRM images of this unusual environment. Several attempts to better understand the physical characteristics of volcanic terrains are described here. Pioneer Venus radar altimeter measurements of topographic variability and surface roughness are compared with Goldstone radar measurements of volcanic terrains on Mars. Synthetic aperture radar images obtained by the SIR-B Space Shuttle experiment over Kilauea Volcano, Hawaii, are employed to investigate the differences in radar returns from pahoehoe, aa and sheet lava flows. Four polarization, multiple incidence angle, aircraft radar images of the Medicine Lake area of N. California are used to address the unusually high cross-polarization ratio of lobate flows around Beta Regio on Venus, as measured by the Arecibo radar.

Mouginis-Mark, P. J.↗
DOE OSTI2023

Portable Programming Model Exploration for LArTPC Simulation in a Heterogeneous Computing Environment: OpenMP vs. SYCL

The evolution of the computing landscape has resulted in the proliferation of diverse hardware architectures, with different flavors of GPUs and other compute accelerators becoming more widely available. To facilitate the efficient use of these architectures in a heterogeneous computing environment, several programming models are available to enable portability and performance across different computing systems, such as Kokkos, SYCL, OpenMP and others. As part of the High Energy Physics Center for Computational Excellence (HEP-CCE) project, we investigate if and how these different programming models may be suitable for experimental HEP workflows through a few representative use cases. One of such use cases is the Liquid Argon Time Projection Chamber (LArTPC) simulation which is essential for LArTPC detector design, validation and data analysis. Following up on our previous investigations of using Kokkos to port LArTPC simulation in the Wire-Cell Toolkit (WCT) to GPUs, we have explored OpenMP and SYCL as potential portable programming models for WCT, with the goal to make diverse computing resources accessible to the LArTPC simulations. In this work, we describe how we utilize relevant features of OpenMP and SYCL for the LArTPC simulation module in WCT. We also show performance benchmark results on multi-core CPUs, NVIDIA and AMD GPUs for both the OpenMP and the SYCL implementations. Comparisons with different compilers will also be given where appropriate.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS2006

Aeolian Shear Stress Ratio Measurements within Mesquite-Dominated Landscapes of the Chihuahuan Desert, New Mexico, USA

A field study was conducted to ascertain the amount of protection that mesquite-dominated communities provide to the surface from wind erosion. The dynamics of the locally accelerated evolution of a mesquite/coppice dune landscape and the undetermined spatial dependence of potential erosion by wind from a shear stress partition model were investigated. Sediment transport and dust emission processes are governed by the amount of protection that can be provided by roughness elements. Although shear stress partition models exist that can describe this, their accuracy has only been tested against a limited dataset because instrumentation has previously been unable to provide the necessary measurements. This study combines the use of meteorological towers and surface shear stress measurements with Irwin sensors to measure the partition of shear stress in situ. The surface shear stress within preferentially aligned vegetation (within coppice dune development) exhibited highly skewed distributions, while a more homogenous surface stress was recorded at a site with less developed coppice dunes. Above the vegetation, the logarithmic velocity profile deduced roughness length (based on 10-min averages) exhibited a distinct correlation with compass direction for the site with vegetation preferentially aligned, while the site with more homogenously distributed vegetation showed very little variation in the roughness length. This distribution in roughness length within an area, defines a distribution of a resolved shear stress partitioning model based on these measurements, ultimately providing potential closure to a previously uncorrelated model parameter.

King, James↗
DOE OSTI2023

Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi

Intimate associations between fungi and intracellular bacterial endosymbionts are becoming increasingly well understood. Phylogenetic analyses demonstrate that bacterial endosymbionts of Mucoromycota fungi are related either to free-living Burkholderia or Mollicutes species. The so-called Burkholderia-related endosymbionts or BRE comprise Mycoavidus, Mycetohabitans and Candidatus Glomeribacter gigasporarum. These endosymbionts are marked by genome contraction thought to be associated with intracellular selection. However, the conclusions drawn thus far are based on a very small subset of endosymbiont genomes, and the mechanisms leading to genome streamlining are not well understood. The purpose of this study was to better understand how intracellular existence shapes Mycoavidus and BRE functionally at the genome level. To this end we generated and analyzed 14 novel draft genomes for Mycoavidus living within the hyphae of Mortierellomycotina fungi. We found that our novel Mycoavidus genomes were significantly reduced compared to free-living Burkholderiales relatives. Using a genome-scale phylogenetic approach including the novel and available existing genomes of Mycoavidus, we show that the genus is an assemblage composed of two independently derived lineages including three well supported clades of Mycoavidus. Using a comparative genomic approach, we shed light on the functional implications of genome reduction, documenting shared and unique gene loss patterns between the three Mycoavidus clades. We found that many endosymbiont isolates demonstrate patterns of vertical transmission and host-specificity, but others are present in phylogenetically disparate hosts. We discuss how reductive evolution and host specificity reflect convergent adaptation to the intrahyphal selective landscape, and commonalities of eukaryotic endosymbiont genome evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2018

The Geology of the Pluto System

NASA's New Horizons mission acquired a large set of images and other data making possible thorough geological analysis of landscapes in the Pluto System. Pluto and Charon exhibit strikingly different surface appearances, despite their similar densities and presumed bulk compositions. Systematic investigation, modelling and mapping revealed that much of Pluto's surface is attributed to surface-atmosphere interactions and the mobilization of volatile ices by insolation. Many mapped valley systems appear to be the consequence of glaciation involving nitrogen ice. Other geological activity requires or required long periods of internal heating, such as Pluto's extensive tectonic fabric. The convection and advection of volatile ices in Sputnik Planitia are thought to be powered by present-day radiogenic heat loss. The prominent mountains at the western margin of Sputnik Planitia, and the strange, multi-km-high mound features to the south, probably composed of H2O, are young geologically as inferred by light cratering and superposition relationships. These multi-km-high mound features might be cryo-volcanoes. Their origin, and what drove their formation so late in Solar System history, is under investigation. East of Sputnik Planitia are large fields of aligned ranks of sharp-crested ridges found only at high altitude that are apparently composed of massive deposits of CH4 ice, referred to as Bladed Terrain. New Horizons found evidence that Bladed Terrain may cover much of Pluto's low latitudes and may have originally formed there as a consequence of Pluto's very high obliquity. Currently Bladed Terrain is undergoing net erosion. This observation, along with evidence for formally more extensive nitrogen glaciation implies that Pluto undergoes significant climate evolution. The dynamic remolding of landscapes by volatile transport seen on Pluto is not unambiguously evident in the mapping of Charon. Charon does, however, display a large resurfaced plain and globally engirdling extensional tectonic network attesting to its early endogenic vigor.

Moore, J. M.↗
NASA NTRS2005

Ice-Ridge Pile Up and the Genesis of Martian "Shorelines"

Unique geomorphologic features such as basin terraces exhibiting topographic continuity have been found within several Martian craters as shown in Viking, MOC, and THEMIS images. These features, showing similarity to terrestrial shorelines, have been mapped and cataloged with significant effort [1]. Currently, open wave action on the surface of paleolakes has been hypothesized as the geomorphologic agent responsible for the generation of these features [2]. As consequence, feature interpretations, including shorelines, wave-cut benches, and bars are, befittingly, lacustrine. Because such interpretations and their formation mechanisms have profound implications for the climate and potential biological history of Mars, confidence is crucial. The insight acquired through linked quantitative modeling of geomorphologic agents and processes is key to accurately interpreting these features. In this vein, recent studies [3,4] involving the water wave energy in theoretical open water basins on Mars show minimal erosional effects due to water waves under Martian conditions. Consequently, sub-glacial lake flattens the surface, produces a local velocity increase over the lake, and creates a deviation of the ice flow from the main flow direction [11]. These consequences of ice flow are observed at Lake Vostok, Antarctica an excellent Martian analogue [11]. Martian observations include reticulate terrain exhibiting sharp inter-connected ridges speculated to reflect the deposition and reworking of ice blocks at the periphery of ice-covered lakes throughout Hellas [12]. Our model determines to what extent ice, a terrestrial geomorphologic agent, can alter the Martian landscape. Method: We study the evolution of crater ice plugs as the formation mechanism of surface features frequently identified as shorelines. In particular, we perform model integrations involving parameters such as ice slope and purity, atmospheric pressure and temperature, crater shape and composition, and an energy balance between solar flux, geothermal flux, latent heat, and ablation. Our ultimate goal is to understand how an intracrater ice plug could create the observed shoreline features and how these

Barnhart, C. J.↗
NASA NTRS2024

Implementation Plan for a NASA Integrated Lunar Science Strategy in the Artemis Era

This Implementation Plan provides a snapshot of NASA’s plans to implement the strategy recommended in OWL and to address the M2M objectives relevant to lunar science. The word “integrated” in the title refers to integrating the capabilities and new opportunities afforded by Artemis and CLPS alongside more traditional mechanisms such as The Discovery and New Frontiers Programs and various Research and Analysis (R&A) elements to achieve our lunar science objectives. It is an opportunity to present the full scope of tools currently available to NASA and how they map to high-priority lunar science that can be accomplished on and at the Moon. It is also an opportunity to build a plan for future NASA-led, lunar focused science and exploration activities that is flexible and can be adapted to a changing landscape (i.e., capability growth, priority evolution, and budgetary fluctuation).

Moon↗
DOE OSTI2024

Pathway Evolution Through a Bottlenecking-Debottlenecking Strategy and Machine Learning-Aided Flux Balancing

The evolution of pathway enzymes enhances the biosynthesis of high-value chemicals, crucial for pharmaceutical, and agrochemical applications. However, unpredictable evolutionary landscapes of pathway genes often hinder successful evolution. Here, the presence of complex epistasis is identifued within the representative naringenin biosynthetic pathway enzymes, hampering straightforward directed evolution. Subsequently, a biofoundry-assisted strategy is developed for pathway bottlenecking and debottlenecking, enabling the parallel evolution of all pathway enzymes along a predictable evolutionary trajectory in six weeks. This study then utilizes a machine learning model, ProEnsemble, to further balance the pathway by optimizing the transcription of individual genes. The broad applicability of this strategy is demonstrated by constructing an Escherichia coli chassis with evolved and balanced pathway genes, resulting in 3.65 g L -1 naringenin. The optimized naringenin chassis also demonstrates enhanced production of other flavonoids. This approach can be readily adapted for any given number of enzymes in the specific metabolic pathway, paving the way for automated chassis construction in contemporary biofoundries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Homologous recombination shapes the architecture and evolution of bacterial genomes

Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores (i.e. replicational halves of circular chromosomes) and most species have genomic hotspots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.

Torrance, Ellis L [University of North Carolina, G↗
DOE OSTI2023

Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics

Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This report will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Mechanisms of Biomolecular Self–Assembly Investigated Through In Situ Observations of Structures and Dynamics

Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. Furthermore, the objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2013

Erosion, Transportation, and Deposition on Outer Solar System Satellites: Landform Evolution Modeling Studies

Mass movement and landform degradation reduces topographic relief by moving surface materials to a lower gravitational potential. In addition to the obvious role of gravity, abrasive mechanical erosion plays a role, often in combination with the lowering of cohesion, which allows disaggregation of the relief-forming material. The identification of specific landform types associated with mass movement and landform degradation provides information about local sediment particle size and abundance and transportation processes. Generally, mass movements can be classified in terms of the particle sizes of the transported material and the speed the material moved during transport. Most degradation on outer planet satellites appears consistent with sliding or slumping, impact erosion, and regolith evolution. Some satellites, such as Callisto and perhaps Hyperion and Iapetus, have an appearance that implies that some additional process is at work, most likely sublimation-driven landform modification and mass wasting. A variant on this process is thermally driven frost segregation as seen on all three icy Galilean satellites and perhaps elsewhere. Titan is unique among outer planet satellites in that Aeolian and fluvial processes also operate to erode, transport, and deposit material. We will evaluate the sequence and extent of various landform-modifying erosional and volatile redistribution processes that have shaped these icy satellites using a 3-D model that simulates the following surface and subsurface processes: 1) sublimation and re-condensation of volatiles; 2) development of refractory lag deposits; 3) disaggregation and downward sloughing of surficial material; 4) radiative heating/cooling of the surface (including reflection, emission, and shadowing by other surface elements); 5) thermal diffusion; and 6) vapor diffusion. The model will provide explicit simulations of landform development and thusly predicts the topographic and volatile evolution of the surface and final landscape form as constrained by DEMs. We have also simulated fluvial and lacustrine modification of icy satellites landscapes to evaluate the degree to which fluvial erosion of representative initial landscapes can replicate the present Titan landscape.

erosion↗
NASA NTRS1992

Fractal landscapes in biological systems: long-range correlations in DNA and interbeat heart intervals

Here we discuss recent advances in applying ideas of fractals and disordered systems to two topics of biological interest, both topics having common the appearance of scale-free phenomena, i.e., correlations that have no characteristic length scale, typically exhibited by physical systems near a critical point and dynamical systems far from equilibrium. (i) DNA nucleotide sequences have traditionally been analyzed using models which incorporate the possibility of short-range nucleotide correlations. We found, instead, a remarkably long-range power law correlation. We found such long-range correlations in intron-containing genes and in non-transcribed regulatory DNA sequences as well as intragenomic DNA, but not in cDNA sequences or intron-less genes. We also found that the myosin heavy chain family gene evolution increases the fractal complexity of the DNA landscapes, consistent with the intron-late hypothesis of gene evolution. (ii) The healthy heartbeat is traditionally thought to be regulated according to the classical principle of homeostasis, whereby physiologic systems operate to reduce variability and achieve an equilibrium-like state. We found, however, that under normal conditions, beat-to-beat fluctuations in heart rate display long-range power law correlations.

Non-NASA Center↗
NASA NTRS2005

Mars, Always Cold, Sometimes Wet: New Constraints on Mars Denudation Rates and Climate Evolution from Analog Studies at Haughton Crater, Devon Island, High Arctic

Analysis of crater modification on Mars and at Haughton Crater, Devon Island, High Arctic, which was recently shown to be significantly older than previously believed (Eocene age instead of Miocene) [1], suggest that Mars may have never been climatically wet and warm for geological lengths of time during and since the Late Noachian. Impact structures offer particularly valuable records of the evolution of a planet s climate and landscape through time. The state of exposure and preservation of impact structures and their intracrater fill provide clues to the nature, timing, and intensity of the processes that have modified the craters since their formation. Modifying processes include weathering, erosion, mantling, and infilling. In this study, we compare the modification of Haughton through time with that of impact craters in the same size class on Mars. We derive upper limits for time-integrated denudation rates on Mars during and since the Late Noachian. These rates are significantly lower than previously published and provide important constraints for Mars climate evolution.

Lee, Pascal↗
NASA NTRS2003

Quantum Adiabatic Optimization and Combinatorial Landscapes

In this paper we analyze the performance of the Quantum Adiabatic Evolution (QAE) algorithm on a variant of Satisfiability problem for an ensemble of random graphs parametrized by the ratio of clauses to variables, gamma = M / N. We introduce a set of macroscopic parameters (landscapes) and put forward an ansatz of universality for random bit flips. We then formulate the problem of finding the smallest eigenvalue and the excitation gap as a statistical mechanics problem. We use the so-called annealing approximation with a refinement that a finite set of macroscopic variables (verses only energy) is used, and are able to show the existence of a dynamic threshold gamma = gammad, beyond which QAE should take an exponentially long time to find a solution. We compare the results for extended and simplified sets of landscapes and provide numerical evidence in support of our universality ansatz.

Smelyanskiy, V. N.↗
NASA NTRS2017

Exploring Connectivity in Sequence Space of Functional RNA

Emergence of replicable genetic molecules was one of the marking points in the origin of life, evolution of which can be conceptualized as a walk through the space of all possible sequences. A theoretical concept of fitness landscape helps to understand evolutionary processes through assigning a value of fitness to each genotype. Then, evolution of a phenotype is viewed as a series of consecutive, single-point mutations. Natural selection biases evolution toward peaks of high fitness and away from valleys of low fitness. whereas neutral drift occurs in the sequence space without direction as mutations are introduced at random. Large networks of neutral or near-neutral mutations on a fitness landscape, especially for sufficiently long genomes, are possible or even inevitable. Their detection in experiments, however, has been elusive. Although a few near-neutral evolutionary pathways have been found, recent experimental evidence indicates landscapes consist of largely isolated islands. The generality of these results, however, is not clear, as the genome length or the fraction of functional molecules in the genotypic space might have been insufficient for the emergence of large, neutral networks. Thorough investigation on the structure of the fitness landscape is essential to understand the mechanisms of evolution of early genomes. RNA molecules are commonly assumed to play the pivotal role in the origin of genetic systems. They are widely believed to be early, if not the earliest, genetic and catalytic molecules, with abundant biochemical activities as aptamers and ribozymes, i.e. RNA molecules capable, respectively, to bind small molecules or catalyze chemical reactions. Here, we present results of our recent studies on the structure of the sequence space of RNA ligase ribozymes selected through in vitro evolution. Several hundred thousands of sequences active to a different degree were obtained by way of deep sequencing. Analysis of these sequences revealed several large clusters defined such that every sequence in a cluster can be reached from any other sequence in the same cluster through a series of single point mutations. Sequences in a single cluster appear to adopt more than one secondary structure. The mechanism of refolding within a single cluster was examined. To shed light on possible evolutionary paths in the space of ribozymes, the connectivity between clusters was investigated. The effect of length of RNA molecules on the structure of the fitness landscape and possible evolutionary paths was examined by way of comparing functional sequences of 20 and 80 nucleobases in length. It was found that sequences of different lengths shared secondary structure motifs that were presumed responsible for catalytic activity, with increasing complexity and global structural rearrangements emerging in longer molecules.

Wei, Chenyu↗