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All sources NASA NTRS DOE OSTI

DOE OSTI2024

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses

Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2018

Adaptive Control Allocation for Powered Descent Vehicles

The following work details a study into real-time failure adaptive control allocation method for powered descent vehicle systems. The motivation for this work is to enable future human and robotic missions utilizing a powered descent system to tolerate engine failures in flight without the loss of crew or assets. This study is conducted using a six degree-of-freedom trajectory simulation of a PDV (Powered Descent Vehicle) experiencing either a loss of thrust or an engine stuck full on failure scenario. Sequential least squares in the frequency domain is used on-board to process inertial measurement unit (IMU) data and generate an estimate of the PDV plant model, which is then fed to the guidance and control system. Data used by the sequential least squares method is generated from an in-flight maneuver. The work herein focuses on determining a maneuver that is least impactful to the PDV trajectory and enables a suitable plant model estimate. A 1.5-second-long maneuver with an amplitude of 5 percent throttle is determined to provide suitable data for the sequential least squares method to estimate a plant model. A PDV implementing this method can adapt to a single engine failure and continue to reach its touchdown conditions.

Green, Justin S.↗

DOE OSTI2024

Study of Microphysical Signatures Based on Spectral Polarimetry during the RELAMPAGO Field Experiment in Argentina

Weather radars with dual-polarization capabilities enable the study of various characteristics of hydrometeors, including their size, shape, and orientation. Radar polarimetric measurements, coupled with Doppler information, allow for analysis in the spectral domain. This analysis can be leveraged to reveal valuable insight into the microphysics and kinematics of hydrometeors in precipitation systems. This paper uses spectral polarimetry to investigate precipitation microphysics and kinematics in storm environments observed during the Remote Sensing of Electrification, Lightning, and Mesoscale/Microscale Processes with Adaptive Ground Observations (RELAMPAGO) field experiment in Argentina. This study uses range–height indicator scan measurements from a C-band polarimetric Doppler weather radar deployed during the field campaign. Here, in this work, the impact of storm dynamics on hydrometeors is studied, including the size sorting of hydrometeors due to vertical wind shear. In addition, particle microphysical processes because of aggregation and growth of ice crystals in anvil clouds, as well as graupel formation resulting from the riming of ice crystals and dendrites, are also analyzed here. The presence of different particle size distributions because of the mixing of hydrometeors in a sheared environment and resulting size sorting has been reported using spectral differential reflectivity (sZ dr ) slope. Spectral reflectivity sZ h and sZ dr have also been used to understand the signature of ice crystal aggregation in an anvil cloud. The regions of pristine ice crystals are identified from vertical profiles of spectral polarimetric variables in anvil cloud because of sZ h < 0 dB and sZ dr values around 2 dB. It is also found that the growth process of these ice crystals causes a skewed bimodal sZ h spectrum due to the presence of both pristine ice crystals and dry snow. Next, graupel formation due to riming has been studied, and it is found that the riming process produces sZ h values of about 10 dB and corresponding sZ dr values of 1 dB. This positive sZ dr indicates the presence of needle/columnar secondary ice particles formed by ice multiplication processes in the riming zones. Last, the temporal evolution of a storm is investigated by analyzing changes in hydrometeor types with time and their influence on the spectral polarimetric variables.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1997

Complex Volume Grid Generation Through the Use of Grid Reusability

This paper presents a set of surface and volume grid generation techniques which reuse existing surface and volume grids. These methods use combinations of data manipulations to reduce grid generation time, improve grid characteristics, and increase the capabilities of existing domain discretization software. The manipulation techniques utilize physical and computational domains to produce basis function on which to operate and modify grid character and smooth grids using Trans-Finite Interpolation, a vector interpolation method and parametric re-mapping technique. With these new techniques, inviscid grids can be converted to viscous grids, multiple zone grid adaption can be performed to improve CFD solver efficiency, and topological changes to improve modeling of flow fields can be done simply and quickly. Examples of these capabilities are illustrated as applied to various configurations.

Alter, Stephen J.↗

DOE OSTI2021

Uniform Subspace Correction Preconditioners for Discontinuous Galerkin Methods with hp-Refinement

In this paper, we develop subspace correction preconditioners for discontinuous Galerkin (DG) discretizations of elliptic problems with hp-refinement. These preconditioners are based on the decomposition of the DG finite element space into a conforming subspace, and a set of small nonconforming edge spaces. The conforming subspace is preconditioned using a matrix-free low-order refined technique, which in this work, we extend to the hp-refinement context using a variational restriction approach. The condition number of the resulting linear system is independent of the granularity of the mesh h, and the degree of the polynomial approximation p. The method is amenable to use with meshes of any degree of irregularity and arbitrary distribution of polynomial degrees. Furthermore, numerical examples are shown on several test cases involving adaptively and randomly refined meshes, using both the symmetric interior penalty method and the second method of Bassi and Rebay (BR2).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Engineered human antibodies for the opsonization and killing of Staphylococcus aureus

Gram-positive organisms with their thick envelope cannot be lysed by complement alone. Nonetheless, antibody-binding on the surface can recruit complement and mark these invaders for uptake and killing by phagocytes, a process known as opsonophagocytosis. The crystallizable fragment of immunoglobulins (Fcγ) is key for complement recruitment. The cell surface of S. aureus is coated with Staphylococcal protein A (SpA). SpA captures the Fcγ domain of IgG and interferes with opsonization by anti-S. aureus antibodies. In principle, the Fcγ domain of therapeutic antibodies could be engineered to avoid the inhibitory activity of SpA. However, the SpA-binding site on Fcγ overlaps with that of the neonatal Fc receptor (FcRn), an interaction that is critical for prolonging the half-life of serum IgG. This evolutionary adaptation poses a challenge for the exploration of Fcγ mutants that can both weaken SpA–IgG interactions and retain stability. Here, we use both wild-type and transgenic human FcRn mice to identify antibodies with enhanced half-life and increased opsonophagocytic killing in models of S. aureus infection and demonstrate that antibody-based immunotherapy can be improved by modifying Fcγ. Our experiments also show that by competing for FcRn-binding, staphylococci effectively reduce the half-life of antibodies during infection. These observations may have profound impact in treating cancer, autoimmune, and asthma patients colonized or infected with S. aureus and undergoing monoclonal antibody treatment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second-strand nicking

R2 retrotransposons are site-specific eukaryotic non–long terminal repeat retrotransposons that copy and paste into gene loci encoding ribosomal RNAs. Recently, we demonstrated that avian A-clade R2 proteins achieve efficient and precise insertion of transgenes into their native safe-harbor loci in human cells. The features of A-clade R2 proteins that support gene insertion are not well characterized. Here, we report high-resolution cryo–electron microscopy structures of two vertebrate A-clade R2 proteins at the initiation of target-primed reverse transcription and after cDNA synthesis and second-strand nicking. Using biochemical and cellular assays, we illuminate the basis for high selectivity of template use and unique roles for each of the three zinc-finger domains in nucleic acid recognition. Reverse transcriptase active site architecture is reinforced by an unanticipated insertion motif specific to vertebrate A-clade R2 proteins. Our work provides the first insights into A-clade R2 protein structure during gene insertion and may enable future improvement and adaptation of R2-based systems for precise transgene insertion.

Science & Technology - Other Topics↗

NASA NTRS1983

Image reconstruction by parametric cubic convolution

Cubic convolution, which has been discussed by Rifman and McKinnon (1974), was originally developed for the reconstruction of Landsat digital images. In the present investigation, the reconstruction properties of the one-parameter family of cubic convolution interpolation functions are considered and thee image degradation associated with reasonable choices of this parameter is analyzed. With the aid of an analysis in the frequency domain it is demonstrated that in an image-independent sense there is an optimal value for this parameter. The optimal value is not the standard value commonly referenced in the literature. It is also demonstrated that in an image-dependent sense, cubic convolution can be adapted to any class of images characterized by a common energy spectrum.

Park, S. K.↗

NASA NTRSDate not supplied

Developing Mars-Based Clinical Scenarios for an Earth Independent Medical Operations (EIMO) – Based Decision Support Service

As crewed missions move beyond Low-Earth Orbit, pre-mission planning cannot fully buy down the medical risks of exploration-class missions. Martian missions, where increased hazards exist, (such as long-duration spaceflight, surface-level EVA operations, and communications delays) will require a paradigm shift in the structure of a medical system. An Earth-Independent Medical Operations-based Medical System (EIMO-MS) will need to optimize four critical domains to help provide medical care: utilization of Pre-Mission Planning, augmentation of Acute and Prolonged Medical Decision Making, automated tracking of Resource Management, and assistance in Task Load Balance. The ideal EIMO-MS will be able to accomplish this goal by having an interactive, adaptable interface that will be able to provide real-time medical services. It must respond based on the level of crewmember training, medical situation, and available medical and non-medical resources. To showcase the capabilities and requirements of such a sophisticated automated MS, a series of clinical scenarios of escalating complexity were developed with clinical and systems engineering input. These scenarios describe in clinical detail what a theoretical future medical system, enhanced with multiple information streams (such as a medical database, an AI-based Decision Support System, real-time monitoring, enhanced in-situ laboratory imaging, etc.) can achieve in conjunction with a trained and experienced crew. Scenarios are comprised of: a context section including objectives and applicable spaceflight environment, a highlighted assumptions section, a clinical narrative section, and a systems engineering activity diagram demonstrating the integrated Medical System (MS). The “swim lanes” of the activity diagram act as the logistical core of each scenario and show how the MS will interact with the crew, ground support, and other in-flight systems. The Design Reference Mission that is used for the scenarios is based on existing reference mission profiles [1] with a projected 30-sol stay on the Martian surface. Scenarios span the spectrum from planned evaluations, minor medical care, urgent care, surgical guidance, critical and expectant management, and behavioral health care. Mission complexity will exponentially increase during deep space and Mars exploration-class missions, and medical support for these missions will likewise need to increase in autonomy and adaptability. The integrated system that will support these missions will need to provide assistance in a variety of anticipated and unforeseen scenarios. These medical scenarios, guided by clinician input, are initial steps in crafting the requirements for an EIMO-based medical system. By working in a systems engineering framework, requirements and capabilities can be extracted and mapped while maintaining a clinical core.

Prashant Parmar↗

DOE OSTI2024

Physics-informed graphical neural network for power system state estimation

State estimation is highly critical for accurately observing the dynamic behavior of the power grids and minimizing risks from cyber threats. However, existing state estimation methods encounter challenges in accurately capturing power system dynamics, primarily because of limitations in encoding the grid topology and sparse measurements. Here, this paper proposes a physics-informed graphical learning state estimation method to address these limitations by leveraging both domain physical knowledge and a graph neural network (GNN). We employ a GNN architecture that can handle the graph-structured data of power systems more effectively than traditional data-driven methods. The physics-based knowledge is constructed from the branch current formulation, making the approach adaptable to both transmission and distribution systems. The validation results of three IEEE test systems show that the proposed method can achieve lower mean square error more than 20% than the conventional methods.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Nonequilibrium DMFT + CPA for correlated disordered systems

We present a solution for the nonequilibrium dynamics of an interacting disordered system. The approach adapts the combination of the equilibrium dynamical mean-field theory and the equilibrium coherent potential approximation methods to the nonequilibrium many-body formalism, using the Kadanoff-Baym-Keldysh complex time contour, for the dynamics of interacting disordered systems away from equilibrium. We use our time domain solution to obtain the equilibrium density of states of the disordered interacting system described by the Anderson-Hubbard model, bypassing the necessity for the cumbersome analytical continuation process. We further apply the nonequilibrium solution to the interaction quench problem for an isolated disordered system. Here, the interaction is abruptly changed from zero (noninteracting system) to another constant (finite) value at which it is subsequently kept. We observe via the time dependence of the potential, kinetic, and total energies the effect of disorder on the relaxation of the system as a function of final interaction strength. Finally, the real-time approach has the potential to shed light on the fundamental role of disorder in the nonequilibrium dynamics of interacting quantum systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS1989

Intelligent Welding Controller

Control system adapts to changing design requirements and operating conditions. Proposed control system for gas/tungsten arc welding requires only that operator specifies such direct parameters of welds as widths and depths of penetration. In control system for robotic welder, components and functions intimately connected with welding process assigned to controller domain. More general functions assigned to supervisor domain. Initial estimate of indirect parameters of welding process applied to system only at beginning of weld (t=0); after start of welding, outputs from multivariable controller takes place of estimate.

Cook, George E.↗

NASA NTRS1990

A unified perspective on robot control - The energy Lyapunov function approach

A unified framework for the stability analysis of robot tracking control is presented. By using an energy-motivated Lyapunov function candidate, the closed-loop stability is shown for a large family of control laws sharing a common structure of proportional and derivative feedback and a model-based feedforward. The feedforward can be zero, partial or complete linearized dynamics, partial or complete nonlinear dynamics, or linearized or nonlinear dynamics with parameter adaptation. As result, the dichotomous approaches to the robot control problem based on the open-loop linearization and nonlinear Lyapunov analysis are both included in this treatment. Furthermore, quantitative estimates of the trade-offs between different schemes in terms of the tracking performance, steady state error, domain of convergence, realtime computation load and required a prior model information are derived.

Wen, John T.↗

NASA NTRS1988

Experimental implementation of adaptive control for flexible space structures

On-going research at The Aerospace Corporation studying the feasibility of applying adaptive control methodologies to the control of flexible space structures is described. A laboratory testbed was established to test system identification and control approaches. The laboratory set-up and controller design approach are discussed. The ARX least squares parameter estimation technique is analyzed in terms of frequency domain transfer function bias error. This analysis approach enables the determination of the effects of sampling rate, sensor type, and data prefiltering on the estimation performance. The ability to identify space structure dynamics over a range of frequencies is shown to be heavily dependent on these factors.

Mcgraw, Gary A.↗

NASA NTRS1998

LOOPREF: A Fluid Code for the Simulation of Coronal Loops

This report documents the code LOOPREF. LOOPREF is a semi-one dimensional finite element code that is especially well suited to simulate coronal-loop phenomena. It has a full implementation of adaptive mesh refinement (AMR), which is crucial for this type of simulation. The AMR routines are an improved version of AMR1D. LOOPREF's versatility makes is suitable to simulate a wide variety of problems. In addition to efficiently providing very high resolution in rapidly changing regions of the domain, it is equipped to treat loops of variable cross section, any non-linear form of heat conduction, shocks, gravitational effects, and radiative loss.

deFainchtein, Rosalinda↗

NASA NTRS1998

Grid Generation Techniques Utilizing the Volume Grid Manipulator

This paper presents grid generation techniques available in the Volume Grid Manipulation (VGM) code. The VGM code is designed to manipulate existing line, surface and volume grids to improve the quality of the data. It embodies an easy to read rich language of commands that enables such alterations as topology changes, grid adaption and smoothing. Additionally, the VGM code can be used to construct simplified straight lines, splines, and conic sections which are common curves used in the generation and manipulation of points, lines, surfaces and volumes (i.e., grid data). These simple geometric curves are essential in the construction of domain discretizations for computational fluid dynamic simulations. By comparison to previously established methods of generating these curves interactively, the VGM code provides control of slope continuity and grid point-to-point stretchings as well as quick changes in the controlling parameters. The VGM code offers the capability to couple the generation of these geometries with an extensive manipulation methodology in a scripting language. The scripting language allows parametric studies of a vehicle geometry to be efficiently performed to evaluate favorable trends in the design process. As examples of the powerful capabilities of the VGM code, a wake flow field domain will be appended to an existing X33 Venturestar volume grid; negative volumes resulting from grid expansions to enable flow field capture on a simple geometry, will be corrected; and geometrical changes to a vehicle component of the X33 Venturestar will be shown.

Alter, Stephen J.↗

NASA NTRS2010

Adaptive Fault Tolerance for Many-Core Based Space-Borne Computing

This paper describes an approach to providing software fault tolerance for future deep-space robotic NASA missions, which will require a high degree of autonomy supported by an enhanced on-board computational capability. Such systems have become possible as a result of the emerging many-core technology, which is expected to offer 1024-core chips by 2015. We discuss the challenges and opportunities of this new technology, focusing on introspection-based adaptive fault tolerance that takes into account the specific requirements of applications, guided by a fault model. Introspection supports runtime monitoring of the program execution with the goal of identifying, locating, and analyzing errors. Fault tolerance assertions for the introspection system can be provided by the user, domain-specific knowledge, or via the results of static or dynamic program analysis. This work is part of an on-going project at the Jet Propulsion Laboratory in Pasadena, California.

fault tolerance↗

NASA NTRS1994

On-line, adaptive state estimator for active noise control

Dynamic characteristics of airframe structures are expected to vary as aircraft flight conditions change. Accurate knowledge of the changing dynamic characteristics is crucial to enhancing the performance of the active noise control system using feedback control. This research investigates the development of an adaptive, on-line state estimator using a neural network concept to conduct active noise control. In this research, an algorithm has been developed that can be used to estimate displacement and velocity responses at any locations on the structure from a limited number of acceleration measurements and input force information. The algorithm employs band-pass filters to extract from the measurement signal the frequency contents corresponding to a desired mode. The filtered signal is then used to train a neural network which consists of a linear neuron with three weights. The structure of the neural network is designed as simple as possible to increase the sampling frequency as much as possible. The weights obtained through neural network training are then used to construct the transfer function of a mode in z-domain and to identify modal properties of each mode. By using the identified transfer function and interpolating the mode shape obtained at sensor locations, the displacement and velocity responses are estimated with reasonable accuracy at any locations on the structure. The accuracy of the response estimates depends on the number of modes incorporated in the estimates and the number of sensors employed to conduct mode shape interpolation. Computer simulation demonstrates that the algorithm is capable of adapting to the varying dynamic characteristics of structural properties. Experimental implementation of the algorithm on a DSP (digital signal processing) board for a plate structure is underway. The algorithm is expected to reach the sampling frequency range of about 10 kHz to 20 kHz which needs to be maintained for a typical active noise control application.

Lim, Tae W.↗