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NASA NTRS2022

Evolution and folding of repeat proteins

Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. These proteins constitute excellent model systems to investigate how evolution relates to structure, folding, and function. Here, we propose a scheme to map evolutionary information at the sequence level to a coarse-grained model for repeat-protein folding and use it to investigate the folding of thousands of repeat proteins. We model the energetics by a combination of an inverse Potts-model scheme with an explicit mechanistic model of duplications and deletions of repeats to calculate the evolutionary parameters of the system at the single-residue level. These parameters are used to inform an Ising-like model that allows for the generation of folding curves, apparent domain emergence, and occupation of intermediate states that are highly compatible with experimental data in specific case studies. We analyzed the folding of thousands of natural Ankyrin repeat proteins and found that a multiplicity of folding mechanisms are possible. Fully cooperative all-or-none transitions are obtained for arrays with enough sequence-similar elements and strong interactions between them, while noncooperative element-by-element intermittent folding arose if the elements are dissimilar and the interactions between them are energetically weak. Additionally, we characterized nucleation-propagation and multidomain folding mechanisms. We show that the global stability and cooperativity of the repeating arrays can be predicted from simple sequence scores.

Ezequiel A. Galpern↗

NASA NTRS1985

Defect-phase-dynamics approach to statistical domain-growth problem of clock models

The growth of statistical domains in quenched Ising-like p-state clock models with p = 3 or more is investigated theoretically, reformulating the analysis of Ohta et al. (1982) in terms of a phase variable and studying the dynamics of defects introduced into the phase field when the phase variable becomes multivalued. The resulting defect/phase domain-growth equation is applied to the interpretation of Monte Carlo simulations in two dimensions (Kaski and Gunton, 1983; Grest and Srolovitz, 1984), and problems encountered in the analysis of related Potts models are discussed. In the two-dimensional case, the problem is essentially that of a purely dissipative Coulomb gas, with a sq rt t growth law complicated by vertex-pinning effects at small t.

Kawasaki, K.↗

NASA NTRS2026

Hybrid Modeling Study on Grain Evolution in the Metal Welding Process and Its Potential Lunar Application

Metal is most commonly used structural material in a wide range of spacecraft, and welding is the principal method for joining metal components into functional systems. However, conducting welding experiments under extreme environments—such as microgravity or vacuum conditions in space—is prohibitively expensive and experimentally challenging. To overcome these limitations, multi-physics computational welding models provide a cost-effective and versatile alternative. In this work, the authors have developed a coupled thermal (fluid) microstructure simulation framework to model metal welding under varying gravity conditions. The framework integrates a mixed-mode heat transfer formulation (conduction, convection, and radiation) with molten pool fluid dynamics, enabling accurate prediction of temperature fields and weld-pool geometry. A grain growth model is further incorporated to capture the spatial and temporal evolution of microstructure, including grain size distribution and morphological transitions during solidification. This approach provides detailed insight into molten pool evolution and grain-level microstructure development throughout the welding process. By explicitly parameterizing environmental conditions, the model supports extrapolation to off-Earth manufacturing scenarios such as welding on the lunar surface. Tantalum—chosen in this study due to its high melting point, oxidation resistance, and mechanical stability at elevated temperatures—serves as the material system for model demonstration. Beyond Tantalum, the integrated multi-physics framework offers broad applicability for predictive welding simulations of various structural and refractory metals or alloys used in extreme terrestrial or extraterrestrial environments.

kinetic Monte Carlo (SPPARKS)↗

NASA NTRS1985

Thermal fields in the Bridgman-Stockbarger technique

Temperature measurements were made throughout a naphthalene melt and solid in a simulated Bridgman-Stockbarger apparatus. Heating and cooling were provided by agitated baths separated by a polymer diaphragm. While agitation was sufficient to give uniform temperatures in the baths, the level of agitation in the heater strongly influenced the results. Unlike theoretical results for high thermal conductivity materials, natural convection in the melt had a strong influence on interface position and on the temperature distribution. Isotherms were relatively flat in the solid and both curved and erratic in the melt. The interface became more convex as it was moved higher into the heating bath by raising either the heating bath or cooling bath temperatures. Using a one-dimensional model, the Biot number in the cooler was determined to be 0.03, that for the solid in the heater 0.008, and for the molten region in the heater 0.3. Biot numbers for two or three dimensional models would be significantly different.

Potts, H.↗

NASA NTRS1987

Transmission of order in some unusual dilute systems

As a system is diluted, the critical temperature T may fall to zero at a concentration X sub c greater than the percolation concentration, because mere connectivity does not guarantee the transmission of order even at T = 0. Detailed results, including bounds on X sub c, are presented for the three-state Potts antiferromagnet on a triangular lattice and for quadrupolar models of (o-H2)x(p-H2)1-x mixtures on fcc and triangular lattices.

Adler, Joan↗

NASA NTRS2026

Modeling Study of Hatch Spacing’s Effect on Grain Morphology in Repairing Damaged Metal Parts with Welding and Hatch Spacing’s Potential Use in Lunar Exploration

The welding process is a potential way of repairing a damaged metal component, especially cavity damage caused by a harsh environment like the lunar environment, which is characterized by large temperature differences and reduced gravity. The adjustment of welding parameter (e.g., hatch spacing) can improve production efficiency in the repair process. Seen from the microstructural level, hatch spacing sensitivity affects the metallic grain evolution and morphology in the welding process, which can further influence a repaired part’s mechanical properties; however, the study of hatch spacing’s effect on microstructure is challenging. Traditional experimental procedures are costly and time-consuming, and any change in hatch spacing value needs roll-back of experimental procedure. A modeling study can address the above challenges in experimental observation. In this research, a modeling approach based on the Kinetic Monte Carlo (KMC) Potts theory was used to simulate grain evolution and morphology with three hatch spacings. Through quantifying and analyzing the predicted grain morphologies, the effect of hatch spacing on microstructure in a welding-fabricated part was investigated. The predicted grain morphologies were validated with an EBSD image of welding microstructure, which has been published before. The primary grain morphologies were columnar grains with a small amount of fine equiaxed grains formed in the scanning path centerline. When increasing the hatch spacing, the columnar grains become larger and more lengthy, while the effect of hatch spacing on the equiaxed grains is not obvious.

Welding for repairing↗

NASA NTRS1988

Requirements analysis, domain knowledge, and design

Two improvements to current requirements analysis practices are suggested: domain modeling, and the systematic application of analysis heuristics. Domain modeling is the representation of relevant application knowledge prior to requirements specification. Artificial intelligence techniques may eventually be applicable for domain modeling. In the short term, however, restricted domain modeling techniques, such as that in JSD, will still be of practical benefit. Analysis heuristics are standard patterns of reasoning about the requirements. They usually generate questions of clarification or issues relating to completeness. Analysis heuristics can be represented and therefore systematically applied in an issue-based framework. This is illustrated by an issue-based analysis of JSD's domain modeling and functional specification heuristics. They are discussed in the context of the preliminary design of simple embedded systems.

Potts, Colin↗

NASA NTRSDate not supplied

Joule-Thomson Cryogenic Nitrogen Orifice Flows

The Joule-Thomson Effect involves the expansion of a fluid through a throttling device, often a simple orifice, resulting in a change in the fluid's temperature. It has been leveraged in the design and analysis of Thermodynamic Vent Systems and integrated into injector designs for cryogenic no-vent fill tank-to-tank transfer testing. There is a scarcity of comprehensive data available to model the phenomenon effectively using tools such as GFSSP for cryogenic nitrogen flows. This experiment aims to model the Joule-Thomson effect of liquid nitrogen through seven traditionally manufactured, sharp-edged orifices manufactured by O’Keefe and three additively manufactured (AM) orifices manufactured by Cumberland Additive. The traditional orifice sizes were 0.016, 0.02, 0.024, 0.032, 0.037, and 0.04 inch in diameter. The three additive orifices had diameters with target/nominal sizes equal to the 0.016, 0.024, and 0.04 inch O’Keefe orifices. However, the actual diameters of the AM orifices were found to be 0.014, 0.024, and 0.035 inches due to additive manufacturing restrictions. Water was flowed through the orifices to verify that their flow coefficients matched published values and to establish flow coefficients for the AM orifices. Liquid nitrogen was flowed through the orifices in a separate test apparatus. The liquid nitrogen started as a subcooled liquid upstream of the orifice and transitioned into a two-phase gas-liquid mixture after passing through each orifice. The upstream pressure was set to 29 psia, 34 psia, 39 psia, and/or 42 psia or 44 psia. The pressure, temperature, and flow rate were measured upstream and downstream of the orifice for three trials at each set point. The average volumetric flow rate and Joule-Thomson Coefficients were calculated from this data. The AM orifices and traditionally manufactured orifices displayed similar results. This data will refine the dataset GFSSP uses to model the J-T Effect more accurately.

Joule-Thomson↗

NASA NTRS1975

Parathyroid hormone, calcitonin, and vitamin D 1974: Present status of physiological studies and analysis of calcium homeostasis

The role of parathyroid hormone, calcitonin, and vitamin D in the control of calcium and bone metabolism was studied. Particular emphasis was placed on the physiological adaptation to weightlessness and, as a potential model for this purpose, on the immobilization characteristic of space flight or prolonged bed rest. The biosynthesis, control of secretion, and metabolism of these hormonal agents is considered.

Potts, J. T., Jr.↗

NASA NTRS1988

Mission design challenges posed by the Voyager 2 Neptune encounter

A major challenge for the Voyager 2 Neptune encounter lies in the detailed design of a trajectory that achieves science objectives at the planet as well as at its large satellite, Triton. This achievement demands a close flyby of the primary, whereas the planet's great distance makes such an undertaking especially challenging. Changing estimates and uncertainties of parameters characterizing the Neptune environment, particularly ring, atmosphere and radiation models, affect the mission design. These effects are investigated and trade-offs among candidate trajectories are examined with respect to spacecraft performance, avoidance of risk and science objective achievement.

Cesarone, R. J.↗

NASA NTRS1999

Detecting Mode Confusion Through Formal Modeling and Analysis

Aircraft safety has improved steadily over the last few decades. While much of this improvement can be attributed to the introduction of advanced automation in the cockpit, the growing complexity of these systems also increases the potential for the pilots to become confused about what the automation is doing. This phenomenon, often referred to as mode confusion, has been involved in several accidents involving modern aircraft. This report describes an effort by Rockwell Collins and NASA Langley to identify potential sources of mode confusion through two complementary strategies. The first is to create a clear, executable model of the automation, connect it to a simulation of the flight deck, and use this combination to review of the behavior of the automation and the man-machine interface with the designers, pilots, and experts in human factors. The second strategy is to conduct mathematical analyses of the model by translating it into a formal specification suitable for analysis with automated tools. The approach is illustrated by applying it to a hypothetical, but still realistic, example of the mode logic of a Flight Guidance System.

Miller, Steven P.↗

NASA NTRS2013

Spiral Arms in the Asymmetrically Illuminated Disk of MWC 758 and Constraints on Giant Planets

We present the first near-IR scattered light detection of the transitional disk associated with the Herbig Ae star MWC 758 using data obtained as part of the Strategic Exploration of Exoplanets and Disks with Subaru, and 1.1 micrometer Hubble Space Telescope/NICMOS data. While submillimeter studies suggested there is a dust-depleted cavity with r = 0".35, we find scattered light as close as 0".1 (20-28 AU) from the star, with no visible cavity at H, K', or Ks . We find two small-scaled spiral structures that asymmetrically shadow the outer disk. We model one of the spirals using spiral density wave theory, and derive a disk aspect ratio of h approximately 0.18, indicating a dynamically warm disk. If the spiral pattern is excited by a perturber, we estimate its mass to be 5(exp +3)(sub -4) M(sub J), in the range where planet filtration models predict accretion continuing onto the star. Using a combination of non-redundant aperture masking data at L' and angular differential imaging with Locally Optimized Combination of Images at K' and Ks , we exclude stellar or massive brown dwarf companions within 300 mas of the Herbig Ae star, and all but planetary mass companions exterior to 0".5. We reach 5 sigma contrasts limiting companions to planetary masses, 3-4 M(sub J) at 1".0 and 2 M(sub J) at 1".55, using the COND models. Collectively, these data strengthen the case for MWC 758 already being a young planetary system.

Grady, C. A.↗

NASA NTRS2005

Satellite Gravity Drilling the Earth

Analysis of satellite-measured gravity and topography can provide crust-to-core mass variation models for new insi@t on the geologic evolution of the Earth. The internal structure of the Earth is mostly constrained by seismic observations and geochemical considerations. We suggest that these constraints may be augmented by gravity drilling that interprets satellite altitude free-air gravity observations for boundary undulations of the internal density layers related to mass flow. The approach involves separating the free-air anomalies into terrain-correlated and -decorrelated components based on the correlation spectrum between the anomalies and the gravity effects of the terrain. The terrain-decorrelated gravity anomalies are largely devoid of the long wavelength interfering effects of the terrain gravity and thus provide enhanced constraints for modeling mass variations of the mantle and core. For the Earth, subcrustal interpretations of the terrain-decorrelated anomalies are constrained by radially stratified densities inferred from seismic observations. These anomalies, with frequencies that clearly decrease as the density contrasts deepen, facilitate mapping mass flow patterns related to the thermodynamic state and evolution of the Earth's interior.

vonFrese, R. R. B.↗

NASA NTRS2004

A Formal Methods Approach to the Analysis of Mode Confusion

The goal of the new NASA Aviation Safety Program (AvSP) is to reduce the civil aviation fatal accident rate by 80% in ten years and 90% in twenty years. This program is being driven by the accident data with a focus on the most recent history. Pilot error is the most commonly cited cause for fatal accidents (up to 70%) and obviously must be given major consideration in this program. While the greatest source of pilot error is the loss of situation awareness , mode confusion is increasingly becoming a major contributor as well. The January 30, 1995 issue of Aviation Week lists 184 incidents and accidents involving mode awareness including the Bangalore A320 crash 2/14/90, the Strasbourg A320 crash 1/20/92, the Mulhouse-Habsheim A320 crash 6/26/88, and the Toulouse A330 crash 6/30/94. These incidents and accidents reveal that pilots sometimes become confused about what the cockpit automation is doing. Consequently, human factors research is an obvious investment area. However, even a cursory look at the accident data reveals that the mode confusion problem is much deeper than just training deficiencies and a lack of human-oriented design. This is readily acknowledged by human factors experts. It seems that further progress in human factors must come through a deeper scrutiny of the internals of the automation. It is in this arena that formal methods can contribute. Formal methods refers to the use of techniques from logic and discrete mathematics in the specification, design, and verification of computer systems, both hardware and software. The fundamental goal of formal methods is to capture requirements, designs and implementations in a mathematically based model that can be analyzed in a rigorous manner. Research in formal methods is aimed at automating this analysis as much as possible. By capturing the internal behavior of a flight deck in a rigorous and detailed formal model, the dark corners of a design can be analyzed. This paper will explore how formal models and analyses can be used to help eliminate mode confusion from flight deck designs and at the same time increase our confidence in the safety of the implementation. The paper is based upon interim results from a new project involving NASA Langley and Rockwell Collins in applying formal methods to a realistic business jet Flight Guidance System (FGS).

Butler, Ricky W.↗

NASA NTRS2014

HD139614: the Interferometric Case for a Group-Ib Pre-Transitional Young Disk

The Herbig Ae star HD139614 is a group-Ib object, which featureless SED indicates disk flaring and a possible pre-transitional evolutionary stage. We present mid- and near-IR interferometric results collected with MIDI, AMBER and PIONIER with the aim of constraining the spatial structure of the 0.1-10 AU disk region and assess its possible multi-component structure. A two-component disk model composed of an optically thin 2-AU wide inner disk and an outer temperature-gradient disk starting at 5.6 AU reproduces well the observations. This is an additional argument to the idea that group-I HAeBe inner disks could be already in the disk-clearing transient stage. HD139614 will become a prime target for mid-IR interferometric imaging with the second-generation instrument MATISSE of the VLTI.

Stellar Interferometry↗

NASA NTRS2013

Evidence of a Discontinuous Disk Structure Around the Herbig Ae Star HD 139614

The formation and evolution of a planetary system are intrinsically linked to the evolution of the primordial accretion disk and its dust and gas content. A new class of pre-main sequence objects has been recently identified as pre-transitional disks. They present near-infrared excess coupled to a flux deficit at about 10 microns and a rising mid-infrared and far-infrared spectrum. These features suggest a disk structure with inner and outer dust components, separated by a dust-depleted region (or gap). This could be the result of particular planet formation mechanisms that occur during the disk evolution. We here report on the first interferometric observations of the disk around the Herbig Ae star HD 139614. Its infrared spectrum suggests a flared disk, and presents pre-transitional features, namely a substantial near-infrared excess accompanied by a dip around 6 microns and a rising mid-infrared part. In this framework, we performed a study of the spectral energy distribution (SED) and the mid-infrared VLTI/MIDI interferometric data to constrain the spatial structure of the inner dust disk region and assess its possibly multi-component structure. We based our work on a temperature-gradient disk model that includes dust opacity.While we could not reproduce the SED and interferometric visibilities with a one-component disk, a better agreement was obtained with a two-component disk model composed of an optically thin inner disk extending from 0.22 to 2.3 AU, a gap, and an outer temperature-gradient disk starting at 5.6 AU. Therefore, our modeling favors an extended and optically thin inner dust component and in principle rules out the possibility that the near-infrared excess originates only from a spatially confined region. Moreover, the outer disk is characterized by a very steep temperature profile and a temperature higher than 300 K at its inner edge. This suggests the existence of a warm component corresponding to a scenario where the inner edge of the outer disk is directly illuminated by the central star. This is an expected consequence of the presence of a gap, thus indicative of a "pre-transitional" structure.

primordial accretion disk↗

NASA NTRS2022

Thermal Imaging of Dust Hiding the Black Hole in NGC 1068

In the widely accepted ‘unified model’1 solution of the classification puzzle of active galactic nuclei, the orientation of a dusty accretion torus around the central black hole dominates their appearance. In ‘type-1’ systems, the bright nucleus is visible at the centre of a face-on torus. In ‘type-2’ systems the thick, nearly edge-on torus hides the central engine. Later studies suggested evolutionary effects2 and added dusty clumps and polar winds3 but left the basic picture intact. However, recent high-resolution images4 of the archetypal type-2 galaxy NGC 10685,6, suggested a more radical revision. The images displayed a ring-like emission feature that was proposed to be hot dust surrounding the black hole at the radius where the radiation from the central engine evaporates the dust. That ring is too thin and too far tilted from edge-on to hide the central engine, and ad hoc foreground extinction is needed to explain the type-2 classification. These images quickly generated reinterpretations of the dichotomy between types 1 and 27,8. Here we present new multi-band mid-infrared images of NGC 1068 that detail the dust temperature distribution and reaffirm the original model. Combined with radio data ( J.F.G. and C.M.V.I., manuscript in preparation), our maps locate the central engine that is below the previously reported ring and obscured by a thick, nearly edge-on disk, as predicted by the unified model. We also identify emission from polar flows and absorbing dust that is mineralogically distinct from that towards the Milky Way centre.

Violeta Gamez Rosas↗

NASA NTRS2003

Crustal Structure of the Iceland Region from Spectrally Correlated Free-air and Terrain Gravity Data

Seismic refraction studies have provided critical, but spatially restricted constraints on the structure of the Icelandic crust. To obtain a more comprehensive regional view of this tectonically complicated area, we spectrally correlated free-air gravity anomalies against computed gravity effects of the terrain for a crustal thickness model that also conforms to regional seismic and thermal constraints. Our regional crustal thickness estimates suggest thickened crust extends up to 500 km on either side of the Greenland-Scotland Ridge with the Iceland-Faeroe Ridge crust being less extended and on average 3-5 km thinner than the crust of the Greenland-Iceland Ridge. Crustal thickness estimates for Iceland range from 25-35 km in conformity with seismic predictions of a cooler, thicker crust. However, the deepening of our gravity-inferred Moho relative to seismic estimates at the thermal plume and rift zones of Iceland suggests partial melting. The amount of partial melting may range from about 8% beneath the rift zones to perhaps 20% above the plume core where mantle temperatures may be 200-400 C above normal. Beneath Iceland, areally limited regions of partial melting may also be compositionally and mechanically layered

Leftwich, T. E.↗