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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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10 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Microsimulation model calibration using incremental mixture approximate Bayesian computation

Microsimulation models (MSMs) are used to inform policy by predicting population-level outcomes under different scenarios. MSMs simulate individual-level event histories that mark the disease process (such as the development of cancer) and the effect of policy actions (such as screening) on these events. MSMs often have many unknown parameters; calibration is the process of searching the parameter space to select parameters that result in accurate MSM prediction of a wide range of targets. We develop Incremental Mixture Approximate Bayesian Computation (IMABC) for MSM calibration which results in a simulated sample from the posterior distribution of model parameters given calibration targets. IMABC begins with a rejection-based ABC step, drawing a sample of points from the prior distribution of model parameters and accepting points that result in simulated targets that are near observed targets. Next, the sample is iteratively updated by drawing additional points from a mixture of multivariate normal distributions and accepting points that result in accurate predictions. Posterior estimates are obtained by weighting the final set of accepted points to account for the adaptive sampling scheme. We demonstrate IMABC by calibrating CRC-SPIN 2.0, an updated version of a MSM for colorectal cancer (CRC) that has been used to inform national CRC screening guidelines.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Algebraic Algorithms for Betweenness and Percolation Centrality

Abstract In this paper, we explored different ways to write the algebraic version of betweenness centrality algorithm. Particularly, we focused on Brandes' algorithm. We aimed for algebraic betweenness centrality that can be parallelized easily. We proposed 3-tuple geodetic semiring as an extension to the usual geodetic semiring with 2-tuples. Using the 3-tuple geodetic semiring, Dijkstra's and Brandes' algorithm, we wrote more concise and general algebraic betweenness centrality (ABC) algorithm which is valid for weighted and directed graphs. We also proposed an alternative version of ABC using the usual geodetic semiring with 2-tuple where we used a simple way to construct shortest path tree after computing shortest path distances in the usual geodetic semiring. This allows us to avoid computational complexity of ABC implementation using 3-tuple geodetic semiring. We used numba to optimize and parallelize ABC. We evaluated the performance of ABC using 2-tuple geodetic semiring as compared to NetworkX, a common python package for graph algorithms. We did scalability experiments on parallel ABC and showed its total speedup. We also showed that with small modification, ABC can be adapted to algebraicly compute other centrality measures such as percolation centrality.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

RANGE: A robust adaptive nature-inspired global explorer of potential energy surfaces

With the growing demand for realistic representations of chemical structures and the advent of exascale computing, the intelligent sampling of potential energy surfaces and efficient identification of global minima have become more essential but also more feasible. Building on prior studies demonstrating the efficiency of the Artificial Bee Colony (ABC) swarm intelligence algorithm, we report a hybrid metaheuristic framework that integrates the adaptive exploration capabilities of ABC coupled with the exploitation strengths of genetic algorithms (GA) in a scalable, Python-based implementation. The resulting tool, RANGE (Robust Adaptive Nature-inspired Global Explorer), provides seamless interfaces to multiple potential energy evaluators, either directly or via widely used Python libraries, and is designed for high-performance computing environments. We describe the implementation details of RANGE and evaluate its performance, relative to ABC- or GA-alone based algorithms, on a variety of chemical systems, including molecular clusters and heterogeneous surfaces. In conclusion, our results demonstrate RANGE’s efficiency, robustness, and broad applicability in addressing challenging global optimization problems in computational chemistry and materials science.

Algorithms and data structure↗
DOE OSTI2020

NWPEsSe: an Adaptive-Learning Global Optimization Algorithm for Nanosized Cluster Systems

Global optimization constitutes an important and fundamental problem in theoretical studies in many chemical fields, such as catalysis, materials or separations problems. In this paper, a novel algorithm has been developed for the global optimization of large systems including neat and ligated clusters in gas phase, and supported clusters in periodic boundary conditions. The method is based on an updated artificial bee colony (ABC) algorithm method, that allows for adaptive-learning during the search process. The new algorithm is tested against four classes of systems of diverse chemical nature: gas phase Au_55, ligated Au_8^(2+), Au_8 supported on graphene oxide and defected rutile, and a large cluster assembly ?[Co?_6 Te_8 (PEt_3 )_6][C_60 ]_n, with sizes ranging between 1 to 3 nm and containing up to 1300 atoms. Reliable global minima (GMs) are obtained for all cases, either confirming published data or reporting new lower energy structures. The algorithm and interface to other codes in the form of an independent program, Northwest Potential Energy Search Engine (NWPEsSe), is freely available and it provides a powerful and efficient approach for global optimization of nanosized cluster systems. The work described in this publication was performed at Pacific Northwest National Laboratory (PNNL), which is operated by Battelle for the United States Department of Energy (DOE) under Contract DE-AC05-76RL0180. J. Z. and V.-A. G. acknowledge support from DOE, Office of Science, Office of Basic Energy Sci-ences, Chemical, Geological and Biological Sciences Division and computing resources from PNNL’s Research Computing Facility and the National Energy Research Scientific Computing Center.

Zhang, Jun↗
NASA NTRS2006

The Origin and Early Evolution of Membrane Proteins

The origin and early evolution of membrane proteins, and in particular ion channels, are considered from the point of view that the transmembrane segments of membrane proteins are structurally quite simple and do not require specific sequences to fold. We argue that the transport of solute species, especially ions, required an early evolution of efficient transport mechanisms, and that the emergence of simple ion channels was protobiologically plausible. We also argue that, despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. These properties can be subtly modulated by local modifications to the sequence rather than global changes in molecular architecture. In order to address the evolution and development of ion channels, we focus on identifying those protein domains that are commonly associated with ion channel proteins and are conserved throughout the three main domains of life (Eukarya, Prokarya, and Archaea). We discuss the potassium-sodium-calcium superfamily of voltage-gated ion channels, mechanosensitive channels, porins, and ABC-transporters and argue that these families of membrane channels have sufficiently universal architectures that they can readily adapt to the diverse functional demands arising during evolution.

Pohorille, Andrew↗
DOE OSTI2020

A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis

Persister cells are genetically identical variants in a bacterial population that have phenotypically modified their physiology to survive environmental stress. In bacterial pathogens, persisters are able to survive antibiotic treatment and reinfect patients in a frustrating cycle of chronic infection. To better define core persistence mechanisms for therapeutics development, we performed transcriptomics analyses of Burkholderia thailandensis populations enriched for persisters via three methods: flow sorting for low proton motive force, meropenem treatment, and culture aging. Although the three persister-enriched populations generally displayed divergent gene expression profiles that reflect the multimechanistic nature of stress adaptations, there were several common gene pathways activated in two or all three populations. These include polyketide and nonribosomal peptide synthesis, Clp proteases, mobile elements, enzymes involved in lipid metabolism, and ATP binding cassette (ABC) transporter systems. In particular, identification of genes that encode polyketide synthases (PKSs) and fatty acid catabolism factors indicates that generation of secondary metabolites, natural products, and complex lipids could be part of the metabolic program that governs the persistence state. We also found that loss-of-function mutations in the PKS-encoding gene locus BTH_I2366, which plays a role in biosynthesis of histone deacetylase (HDAC) inhibitors, resulted in increased sensitivity to antibiotics targeting DNA replication. Furthermore, treatment of multiple bacterial pathogens with a fatty acid synthesis inhibitor, CP-640186, potentiated the efficacy of meropenem against the persister populations. Altogether, our results suggest that bacterial persisters may exhibit an outwardly dormant physiology but maintain active metabolic processes that are required to maintain persistence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Clostridioides difficile utilizes siderophores as an iron source and FhuDBGC contributes to ferrichrome uptake

ABSTRACT Clostridioides difficileremains a public health threat commonly observed following antibiotic use. Due to the importance of iron in many cell processes, most bacteria, includingC. difficile, have multiple mechanisms of acquiring iron. Previous studies have examined ferrous iron uptake inC. difficile; here we focus on the role of siderophores. In a growth assay, we show thatC. difficilecan use a variety of siderophores as the sole iron source. InC. difficile,two ABC transporters induced under low iron conditions are predicted siderophore importers: FhuDBGC and YclNOPQ. We hypothesized that these transporters are responsible for the uptake of the siderophores we tested. To investigate the specificity of these transporters, we purified the substrate binding proteins and examined siderophore binding using thermal shift. We demonstrate increased stability between one siderophore binding protein, FhuD, and the siderophore ferrichrome, suggesting a binding interaction. This specificity correlates with the inability of anΔfhuDBGCmutant to grow efficiently under iron limiting conditions in the presence of ferrichrome. WhileC. difficileused additional siderophores in our growth experiments, we did not observe increased thermal stability between the receptor proteins and any of the other siderophores tested, suggesting these siderophores do not bind these receptors and other siderophore import mechanisms remain to be elucidated. Redundancy in iron acquisition is a microbial survival adaptation to cope with the constant battle for iron within a host. Greater knowledge about howC. difficileacquires iron will provide insight about howC. difficilecolonizes and persists in the colon. IMPORTANCE This study is the first example ofC. difficilegrowing with siderophores as the sole iron source and describes the characterization of the ferric hydroxamate uptake ABC transporter (FhuDBGC). This transporter shows specificity to the siderophore ferrichrome. While not required for pathogenesis, this transporter highlights the redundancy in iron acquisition mechanisms thatC. difficileuses to compete for iron during an infection.

Microbiology↗
NASA NTRS1994

Investigation of finite element: ABC methods for electromagnetic field simulation

The mechanics of wave propagation in the presence of obstacles is of great interest in many branches of engineering and applied mathematics like electromagnetics, fluid dynamics, geophysics, seismology, etc. Such problems can be broadly classified into two categories: the bounded domain or the closed problem and the unbounded domain or the open problem. Analytical techniques have been derived for the simpler problems; however, the need to model complicated geometrical features, complex material coatings and fillings, and to adapt the model to changing design parameters have inevitably tilted the balance in favor of numerical techniques. The modeling of closed problems presents difficulties primarily in proper meshing of the interior region. However, problems in unbounded domains pose a unique challenge to computation, since the exterior region is inappropriate for direct implementation of numerical techniques. A large number of solutions have been proposed but only a few have stood the test of time and experiment. The goal of this thesis is to develop an efficient and reliable partial differential equation technique to model large three dimensional scattering problems in electromagnetics.

Chatterjee, A.↗
DOE OSTI2021

Generation of Pseudomonas putida KT2440 Strains with Efficient Utilization of Xylose and Galactose via Adaptive Laboratory Evolution

While Pseudomonas putida KT2440 has great potential for biomass-converting processes, its inability to utilize the biomass abundant sugars xylose and galactose has limited its applications. Here, in this study, we utilized Adaptive Laboratory Evolution (ALE) to optimize engineered KT2440 with heterologous expression of xylD encoding xylonate dehydratase from Caulobacter crescentus and galETKM encoding UDP-glucose 4-epimerase, galactose-1-phosphate uridylyltransferase, galactokinase, and galactose-1-epimerase from Escherichia coli K-12 MG1655. Poor starting strain growth (<0.1 h –1 or none) was evolutionarily optimized to rates of up to 0.25 h –1 on xylose and 0.52 h –1 on galactose. Whole-genome sequencing, transcriptomic analysis, and growth screens revealed significant roles of kguT encoding a 2-ketogluconate operon repressor and 2-ketogluconate transporter, and gtsABCD encoding an ATP-binding cassette (ABC) sugar transporting system in xylose and galactose growth conditions, respectively. Finally, we expressed the heterologous indigoidine production pathway in the evolved and unevolved engineered strains and successfully produced 3.2 g/L and 2.2 g/L from 10 g/L of either xylose or galactose in the evolved strains whereas the unevolved strains did not produce any detectable product. Thus, the generated KT2440 strains have the potential for broad application as optimized platform chassis to develop efficient microorganism-based biomass-utilizing bioprocesses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

Uncrewed Lunar Surface Operations and Support Activities

Sustained human presence on the surface of the Moon and future missions to Mars require increased independence from surface crews and Earth-based mission control to operate efficiently, safely, and reliably. The time for surface crews to perform tasks will be limited. Extravehicular activities by surface personnel are burdensome and time-consuming, even when a continuous human presence on the surface occurs. Identifying and balancing human/automation roles and tasks and infusing automation and autonomy practices early in a system’s lifecycle will be essential to achieve mission objectives. Among these objectives are attaining a sustained human presence, improving performance and mission effectiveness, reducing operations and maintenance (O&M) costs, and ensuring operations that are robust to communication delays. To achieve these objectives, an operational shift toward increased automation and autonomy with less reliance on humans is needed. Uncrewed lunar surface operations and support activities occur when surface crews are not present or are independent of surface crew timeline activities requiring no surface crew oversight or intervention. These uncrewed surface opportunities can also be planned to minimize crew workload that avoids routine maintenance and support tasks, thus maximizing crew exploration time. Uncrewed preparations such as staging and prepositioning equipment and materials before the crew arrives could improve crew task efficiency. Additional opportunities exist to conduct uncrewed science, exploration, and utilization. Uncrewed surface architecture functions can include science and exploration; habitation; launch and landing support; surface communication and navigation; surface power generation and distribution; human surface mobility; lifting, handling, manipulating; excavation, construction, and site preparation; logistics management; maintenance and repair; surface resource utilization; integrated site operations and shared support services (e.g., site scheduling/prioritization, dust mitigation/contamination control, and surface safety). Early robotic lunar surface campaigns will provide information on the availability of resources, such as oxygen and water, and demonstrate surface-based technologies. After the Artemis III human lunar return mission, a series of landers will deliver surface systems, cargo, supplies, science packages, spare parts, and commodities. A balance of crewed and uncrewed surface operations will enable a sustained lunar surface presence at the South Pole of the Moon at a site that will be known as the Artemis Base Camp (ABC). It is envisioned that base camp operations on and around the Moon will then help prepare for the mission durations and activities needed to support the first human mission to Mars. Before long-duration crew missions to the base camp can occur, the necessary surface infrastructure will be pre-deployed and verified operational. Surface assets will be teleoperated and remotely managed from Earth. Additionally, robotic and short-duration crewed missions to the ABC will ensure the site’s merit to achieve long-term science objectives, availability of usable resources, and that terrain, seasonal variations, and illumination conditions are acceptable. ABC will consist of different areas where specific functions and services are rendered, including: • Launch and Landing Area • Habitation Area • Power Production Area • Resource Areas Launch and Landing Area—The launch and landing area will support associated functions for the arrival and departure of vehicles, such as crewed landing and ascent and uncrewed cargo deliveries and offloading. It will evolve from an unimproved site at the beginning of the exploration campaign to a more sustainable landing and launch area that can support repeated arrivals and departures. Initial uncrewed Lunar Terrain Vehicle (LTV) surface operations may include emplacement of navigation beacons and communication equipment, real-time video and photography of landing/liftoff events, and element repositioning, such as portable utility power (PUP) (applicable for other landed assets at other areas). Site preparations, such as surface leveling, soil compaction, and berm/path construction, may be needed for a more sustainable launch and landing area capable of accommodating vehicles that are increasingly more reusable and reduce the effects of plume surface interactions and ejecta impacts on nearby surface assets. During the ABC missions, cargo and logistics will be delivered to the lunar surface via robotic cargo landers before the crew arrives. These shipments, which can arrive in pressurized logistics carriers, will deliver the logistics necessary to support a crewed mission and include items such as food, water, equipment spares, etc. Providing the capability to retrieve, offload, and transport the logistics closer to the ABC site before the arrival of the crew will increase the overall efficiency of crew operations once they arrive. In the sustained phase of exploration, other supporting services may be needed, such as lander propellant servicing, surface power services, commodity refreshes, and additional inspection, maintenance, and repair capabilities, to sustain a cadence of extended personnel stays and cargo arrivals and departures. Habitation Area—Uncrewed support to surface habitation could involve supporting activation and pre-entry operations of the habitat while the crew is in orbit at the Gateway outpost preparing for a surface landing. Surface Habitat (SH) uncrewed operations may include bringing the cabin environment to a habitable temperature and air mix and activating other critical crew support systems. Potential crop production uncrewed tasks in the SH could also include autonomous watering and tending. Additionally, when the crew departs, the SH enters dormancy for the long period of uncrewed operation. A logistical staging area could also be collocated near the SH. If so, staging operations for crew supplies, waste re-location, and recycling operations may be opportunities for uncrewed operations. Power Production Area—The Fission Surface Power (FSP) element and its supporting distribution equipment provide power to surface elements as needed across the ABC to supplement day-to-day operations and survive lunar nights. Uncrewed support of this power system includes any initial LTV-assisted deployments of cables and other distributed equipment, associated electrical connections, and system testing and activation operations. Robotically performing some inspections, maintenance, or repair tasks on the power distribution equipment could reduce the surface crew workload. Resource Area— Uncrewed resource prospecting, mapping, and characterizing possible resource sites is likely to be time-consuming and represents an opportunity for uncrewed operations between crewed missions. Uncrewed mobile equipment operations will be needed in the extreme environments of permanently shadowed locations where resource extractions occur. As In-Situ Resource Utilization (ISRU) pilot plant operations begin, uncrewed surface support activities with available mobile and portable assets (LTV, PUP, etc.) will better support these operations. Any produced commodities can be stored at a centralized storage location for future use. Also associated with these operations is the use of mobile robotic excavators for resource acquisition and robotic/autonomous regolith processing. The waste tailings generated during excavation and regolith processing would also need to be transported and deposited at a dedicated location. Surface assets will continue operating between crew visits to maintain surface capabilities, conduct lunar surface science, technology demonstrations, and public outreach opportunities. Additionally, certain sustaining tasks that would consume valuable crew time could be performed before crew arrival, or after their departure. This capability may offer more affordable options to construct, activate, test, and maintain a broad set of surface assets. Telerobotically operated human surface mobility systems, such as the LTV and Pressurized Rover (PR), can be utilized for various tasks. Surface environmental conditions pose a distinct challenge for all these activities. Surface illumination and localized shadows are one such factor. Night-survival operations could consist of thermal management, battery pre-charging, and load shedding. Some surface systems may hibernate through the night and then awake and continue nominal operations. Uncrewed mobile assets may use a more adaptive approach to optimize their power and operations; one method is to follow the sunlight. Night-survival operations may be initiated remotely by teleoperation, automated, or accomplished by supervised autonomous operation. The ability to pre-deploy and control remote assets in orbit or on Mars before the arrival of the mission crew is a key capability that can be simulated on the moon. The base camp provides a venue where these advanced operational concepts, technologies, and autonomous methods and techniques, including the incorporation of time delays to simulate Earth-Mars latency can be replicated to help buy down future Mars mission risks. This paper will examine the evolution of uncrewed lunar surface operations and support activities. It will also discuss the lunar surface environmental conditions (thermal, lighting, terrain, topography, communications) along with the challenges they pose on uncrewed surface operations, and the performance of these activities with limited to minimal human interaction and/or teleoperation. Since lunar missions include Mars mission analogs, such investigation provides the framework for future uncrewed Mars mission support.

Mark E Lewis↗