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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

Geometric basis for the far red shift

An alternative explanation is offered for the redshift (an abrupt change in the ratio of scattering to absorption in the radiance spectra of heading canopies of such crops as wheat and grain sorghum). The shift occurs abruptly at wavelengths near the red-infrared boundary towards the longer wavelengths. The new explanation, following that of Collins (1978) and Schutt et al. (1984), is based on one particular architectural change that occurs in any heading plant canopy. Specifically, the newly extended heads alter the interaction between light and the established foliage. The heads reduce the amount of sunlight striking the topmost leaves which are generally comparatively good specular reflectors. The heads also reduce the ability to observe the specularly reflecting leaves. The reduction in the amplitude of the radiance (due to decreased specularly reflected light) at heading appears to be a shift in the wavelength of the red edge. It is proposed that vertical (amplitude) shifts - due to changes in the amount of specularly reflected light as a function of heading - have been misinterpreted as horizontal (wavelength) shifts due in part to the characteristic shape of the radiance curve at the red edge.

Vanderbilt, V. C.↗

NASA NTRS1997

A Multi-Level Parallelization Concept for High-Fidelity Multi-Block Solvers

The integration of high-fidelity Computational Fluid Dynamics (CFD) analysis tools with the industrial design process benefits greatly from the robust implementations that are transportable across a wide range of computer architectures. In the present work, a hybrid domain-decomposition and parallelization concept was developed and implemented into the widely-used NASA multi-block Computational Fluid Dynamics (CFD) packages implemented in ENSAERO and OVERFLOW. The new parallel solver concept, PENS (Parallel Euler Navier-Stokes Solver), employs both fine and coarse granularity in data partitioning as well as data coalescing to obtain the desired load-balance characteristics on the available computer platforms. This multi-level parallelism implementation itself introduces no changes to the numerical results, hence the original fidelity of the packages are identically preserved. The present implementation uses the Message Passing Interface (MPI) library for interprocessor message passing and memory accessing. By choosing an appropriate combination of the available partitioning and coalescing capabilities only during the execution stage, the PENS solver becomes adaptable to different computer architectures from shared-memory to distributed-memory platforms with varying degrees of parallelism. The PENS implementation on the IBM SP2 distributed memory environment at the NASA Ames Research Center obtains 85 percent scalable parallel performance using fine-grain partitioning of single-block CFD domains using up to 128 wide computational nodes. Multi-block CFD simulations of complete aircraft simulations achieve 75 percent perfect load-balanced executions using data coalescing and the two levels of parallelism. SGI PowerChallenge, SGI Origin 2000, and a cluster of workstations are the other platforms where the robustness of the implementation is tested. The performance behavior on the other computer platforms with a variety of realistic problems will be included as this on-going study progresses.

Hatay, Ferhat F.↗

NASA NTRS2018

Molecular Dynamics Simulations of Liquid and Polymer Electrolytes for Energy Storage Devices

Advancing beyond current lithium-ion technology is necessary in order to enable energy storage devices for electric airplanes. Electrolyte stability is a key limiting factor, yet the design of improved electrolytes remains a formidable challenge. Molecular dynamics (MD) simulations are a powerful tool for studying electrolytes, since they can be used to evaluate structural, thermodynamic, and transport properties, and can provide molecular-level detail often inaccessible to experimental techniques. Our computational materials groups at the NASA Ames Research Center has developed models and methods to accurately simulate both liquid and polymer electrolytes.We report the results from atomistic MD simulations of several electrolyte materials, with lithium salts dissolved in ionic liquids, dimethoxyethane (DME), and polyethylene oxide (PEO). For improved accuracy, we employ polarizable models, where each atom is given an environment-dependent atomic dipole. The simulations accurately predict bulk transport properties, including viscosity, diffusion, and ionic conductivity, in quantitative agreement with available experimental data. Moreover, the simulations provide important insights into the solvation structure of the lithium ions.We also report the results from coarse-grained MD simulations of polyanion electrolytes. In order to more efficiently capture the longer length- and time-scales of these systems, we employ a generic bead-spring model. These simulations provide important insight into how the polymer chain architecture and ionic interaction strengths affect the ionic aggregation behavior and cation dynamics. Despite the simplicity of the model, the simulations yield qualitative agreement with experimental data for similar systems.

Abbott, Lauren J.↗

NASA NTRS2021

Aqua Factorem: Ultra Low Energy Lunar Water Extraction

We propose a new method we call Aqua Factorem to extract lunar water. It will drastically reduce energy and complexity of lunar mining operations helping to establish this industry. Other methods to extract water from the regolith are based on phase change, pumping energy into the regolith to sublimate the ice into vapor, then capturing the vapor, re-freezing it, and hauling the solid ice to a chemical processor where it is converted again into vapor for purification then electrolysis. This requires transporting high power into the permanently shadowed regions (PSRs) not only to vaporize the ice in situ in the soil but to heat the surrounding soil itself, which is wasted energy. Still other methods are based on strip mining and hauling the resource along with slag (the unwanted silicates, which constitutes about 95% of the mass), to a processing unit that is located outside the PSRs. That may be a simpler architecture but is generally not favored because hauling 49,000 t of regolith over many kilometers yearly to produce the projected demand of 2,450 t of propellant would be terribly difficult and expensive with high risk that the vehicles will get stuck driving with such loads across the unprepared regolith. We propose an alternative to both of these approaches, taking advantage of the processing that the unique lunar geology has already performed. Micrometeoroid bombardment has already broken most solid material in the upper part of the regolith into fine grains. This includes solid material of all compositions, including the ice, which is as hard as granite at PSR temperatures and is therefore essentially another type of rock. These ice grains are intermixed with all the other minerals, so a simple, ultra-low-energy grain-sorting process can extract the ice without phase change. As another benefit it can extract the 1 wt% free metal known to be in lunar soil, again with very little energy. The ice can then be hauled to the chemical processing unit in solid phase and converted into rocket propellant. We estimate the 800 kW power needed for thermal extraction can be reduced to less than 100 watts using the new method. This affects the entire architecture of the mining operation producing extensive economic benefit, which we will quantify in this study. We will study it in the context of a mission to mine propellants commercially for space tugs that boost commercial communication satellites from Geosynchronous Transfer Orbit (GTO) to Geostationary Orbit (GEO) then return to the lunar surface for refueling. This simple architecture requires the minimum number of in-space elements, and notably does not require an in-space propellant depot, so it provides the lowest cost and lowest risk startup for a commercial operation. The study will also test the innovative Aqua Factorem process through laboratory experiments, and this will produce basic insights into the handling of lunar resources.

lunar↗

NASA NTRS1989

Group implicit concurrent algorithms in nonlinear structural dynamics

During the 70's and 80's, considerable effort was devoted to developing efficient and reliable time stepping procedures for transient structural analysis. Mathematically, the equations governing this type of problems are generally stiff, i.e., they exhibit a wide spectrum in the linear range. The algorithms best suited to this type of applications are those which accurately integrate the low frequency content of the response without necessitating the resolution of the high frequency modes. This means that the algorithms must be unconditionally stable, which in turn rules out explicit integration. The most exciting possibility in the algorithms development area in recent years has been the advent of parallel computers with multiprocessing capabilities. So, this work is mainly concerned with the development of parallel algorithms in the area of structural dynamics. A primary objective is to devise unconditionally stable and accurate time stepping procedures which lend themselves to an efficient implementation in concurrent machines. Some features of the new computer architecture are summarized. A brief survey of current efforts in the area is presented. A new class of concurrent procedures, or Group Implicit algorithms is introduced and analyzed. The numerical simulation shows that GI algorithms hold considerable promise for application in coarse grain as well as medium grain parallel computers.

Ortiz, M.↗

NASA NTRS2021

The Enceladus Orbilander Mission Concept: Balancing Return and Resources in the Search for Life

Enceladus’s long-lived plume of ice grains and water vapor makes accessing oceanic material readily achievable from orbit (around Saturn or Enceladus) and from the moon’s surface. In preparation for the National Academies of Sciences, Engineering and Medicine 2023–2032 Planetary Science and Astrobiology Decadal Survey, we investigated four architectures capable of collecting and analyzing plume material from orbit and/or on the surface to address the most pressing questions at Enceladus: Is the subsurface ocean inhabited? Why, or why not? Trades specific to these four architectures were studied to allow an evaluation of the science return with respect to investment. The team found that Orbilander, a mission concept that would first orbit and then land on Enceladus, represented the best balance. Orbilander was thus studied at a higher fidelity, including a more detailed science operations plan during both orbital and landed phases, landing site characterization and selection analyses, and landing procedures. The Orbilander mission concept demonstrates that scientifically compelling but resource-conscious Flagship-class missions can be executed in the next decade to search for life at Enceladus.

Shannon M. MacKenzie↗

NASA NTRS2010

BioNet Digital Communications Framework

BioNet v2 is a peer-to-peer middleware that enables digital communication devices to talk to each other. It provides a software development framework, standardized application, network-transparent device integration services, a flexible messaging model, and network communications for distributed applications. BioNet is an implementation of the Constellation Program Command, Control, Communications and Information (C3I) Interoperability specification, given in CxP 70022-01. The system architecture provides the necessary infrastructure for the integration of heterogeneous wired and wireless sensing and control devices into a unified data system with a standardized application interface, providing plug-and-play operation for hardware and software systems. BioNet v2 features a naming schema for mobility and coarse-grained localization information, data normalization within a network-transparent device driver framework, enabling of network communications to non-IP devices, and fine-grained application control of data subscription band width usage. BioNet directly integrates Disruption Tolerant Networking (DTN) as a communications technology, enabling networked communications with assets that are only intermittently connected including orbiting relay satellites and planetary rover vehicles.

Gifford, Kevin↗

NASA NTRS2013

Coarse-Grain Bandwidth Estimation Techniques for Large-Scale Space Network

In this paper, we describe a top-down analysis and simulation approach to size the bandwidths of a store-andforward network for a given network topology, a mission traffic scenario, and a set of data types with different latency requirements. We use these techniques to estimate the wide area network (WAN) bandwidths of the ground links for different architecture options of the proposed Integrated Space Communication and Navigation (SCaN) Network.

Cheung, Kar-Ming↗

NASA NTRS2000

Bioelectric Control of a 757 Class High Fidelity Aircraft Simulation

This paper presents results of a recent experiment in fine grain Electromyographic (EMG) signal recognition, We demonstrate bioelectric flight control of 757 class simulation aircraft landing at San Francisco International Airport. The physical instrumentality of a pilot control stick is not used. A pilot closes a fist in empty air and performs control movements which are captured by a dry electrode array on the arm, analyzed and routed through a flight director permitting full pilot outer loop control of the simulation. A Vision Dome immersive display is used to create a VR world for the aircraft body mechanics and flight changes to pilot movements. Inner loop surfaces and differential aircraft thrust is controlled using a hybrid neural network architecture that combines a damage adaptive controller (Jorgensen 1998, Totah 1998) with a propulsion only based control system (Bull & Kaneshige 1997). Thus the 757 aircraft is not only being flown bioelectrically at the pilot level but also demonstrates damage adaptive neural network control permitting adaptation to severe changes in the physical flight characteristics of the aircraft at the inner loop level. To compensate for accident scenarios, the aircraft uses remaining control surface authority and differential thrust from the engines. To the best of our knowledge this is the first time real time bioelectric fine-grained control, differential thrust based control, and neural network damage adaptive control have been integrated into a single flight demonstration. The paper describes the EMG pattern recognition system and the bioelectric pattern recognition methodology.

Jorgensen, Charles↗

NASA NTRS1989

A language comparison for scientific computing on MIMD architectures

Choleski's method for solving banded symmetric, positive definite systems is implemented on a multiprocessor computer using three FORTRAN based parallel programming languages, the Force, PISCES and Concurrent FORTRAN. The capabilities of the language for expressing parallelism and their user friendliness are discussed, including readability of the code, debugging assistance offered, and expressiveness of the languages. The performance of the different implementations is compared. It is argued that PISCES, using the Force for medium-grained parallelism, is the appropriate choice for programming Choleski's method on the multiprocessor computer, Flex/32.

Jones, Mark T.↗

NASA NTRS1992

Parallel fault-tolerant robot control

A shared memory multiprocessor architecture is used to develop a parallel fault-tolerant robot controller. Several versions of the robot controller are developed and compared. A robot simulation is also developed for control observation. Comparison of a serial version of the controller and a parallel version without fault tolerance showed the speedup possible with the coarse-grained parallelism currently employed. The performance degradation due to the addition of processor fault tolerance was demonstrated by comparison of these controllers with their fault-tolerant versions. Comparison of the more fault-tolerant controller with the lower-level fault-tolerant controller showed how varying the amount of redundant data affects performance. The results demonstrate the trade-off between speed performance and processor fault tolerance.

Hamilton, D. L.↗

NASA NTRS1995

Algorithms for parallel flow solvers on message passing architectures

The purpose of this project has been to identify and test suitable technologies for implementation of fluid flow solvers -- possibly coupled with structures and heat equation solvers -- on MIMD parallel computers. In the course of this investigation much attention has been paid to efficient domain decomposition strategies for ADI-type algorithms. Multi-partitioning derives its efficiency from the assignment of several blocks of grid points to each processor in the parallel computer. A coarse-grain parallelism is obtained, and a near-perfect load balance results. In uni-partitioning every processor receives responsibility for exactly one block of grid points instead of several. This necessitates fine-grain pipelined program execution in order to obtain a reasonable load balance. Although fine-grain parallelism is less desirable on many systems, especially high-latency networks of workstations, uni-partition methods are still in wide use in production codes for flow problems. Consequently, it remains important to achieve good efficiency with this technique that has essentially been superseded by multi-partitioning for parallel ADI-type algorithms. Another reason for the concentration on improving the performance of pipeline methods is their applicability in other types of flow solver kernels with stronger implied data dependence. Analytical expressions can be derived for the size of the dynamic load imbalance incurred in traditional pipelines. From these it can be determined what is the optimal first-processor retardation that leads to the shortest total completion time for the pipeline process. Theoretical predictions of pipeline performance with and without optimization match experimental observations on the iPSC/860 very well. Analysis of pipeline performance also highlights the effect of uncareful grid partitioning in flow solvers that employ pipeline algorithms. If grid blocks at boundaries are not at least as large in the wall-normal direction as those immediately adjacent to them, then the first processor in the pipeline will receive a computational load that is less than that of subsequent processors, magnifying the pipeline slowdown effect. Extra compensation is needed for grid boundary effects, even if all grid blocks are equally sized.

Vanderwijngaart, Rob F.↗

NASA NTRS1996

Research in Parallel Algorithms and Software for Computational Aerosciences

Phase 1 is complete for the development of a computational fluid dynamics CFD) parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.

Domel, Neal D.↗

NASA NTRS1996

Research in Parallel Algorithms and Software for Computational Aerosciences

Phase I is complete for the development of a Computational Fluid Dynamics parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.

Domel, Neal D.↗

NASA NTRS2013

Asteroid Belts in Debris Disk Twins: Vega and Fomalhaut

Vega and Fomalhaut are similar in terms of mass, ages, and global debris disk properties; therefore, they are often referred to as debris disk twins. We present Spitzer 10-35 micrometers spectroscopic data centered at both stars and identify warm, unresolved excess emission in the close vicinity of Vega for the first time. The properties of the warm excess in Vega are further characterized with ancillary photometry in the mid-infrared and resolved images in the far-infrared and submillimeter wavelengths. The Vega warm excess shares many similar properties with the one found around Fomalhaut. The emission shortward of approximately 30 micrometers from both warm components is well described as a blackbody emission of approximately 170 K. Interestingly, two other systems, Eri and HR 8799, also show such an unresolved warm dust using the same approach. These warm components may be analogous to the solar system s zodiacal dust cloud, but of far greater mass (fractional luminosity of approximately 10(exp-5) to 10(exp-6) compared to 10(exp-8) to 10(exp-7). The dust temperature and tentative detections in the submillimeter suggest that the warm excess arises from dust associated with a planetesimal ring located near the water-frost line and presumably created by processes occurring at similar locations in other debris systems as well. We also review the properties of the 2 micrometers hot excess around Vega and Fomalhaut, showing that the dust responsible for the hot excess is not spatially associated with the dust we detected in the warm belt.We suggest it may arise from hot nano grains trapped in the magnetic field of the star. Finally, the separation between the warm and cold belt is rather large with an orbital ratio greater than or approximately 10 in all four systems. In light of the current upper limits on the masses of planetary objects and the large gap, we discuss the possible implications for their underlying planetary architecture and suggest that multiple, low-mass planets likely reside between the two belts in Vega and Fomalhaut.

Su, Kate Y. L.↗

NASA NTRS1994

Using CLIPS in the domain of knowledge-based massively parallel programming

The Program Development Environment (PDE) is a tool for massively parallel programming of distributed-memory architectures. Adopting a knowledge-based approach, the PDE eliminates the complexity introduced by parallel hardware with distributed memory and offers complete transparency in respect of parallelism exploitation. The knowledge-based part of the PDE is realized in CLIPS. Its principal task is to find an efficient parallel realization of the application specified by the user in a comfortable, abstract, domain-oriented formalism. A large collection of fine-grain parallel algorithmic skeletons, represented as COOL objects in a tree hierarchy, contains the algorithmic knowledge. A hybrid knowledge base with rule modules and procedural parts, encoding expertise about application domain, parallel programming, software engineering, and parallel hardware, enables a high degree of automation in the software development process. In this paper, important aspects of the implementation of the PDE using CLIPS and COOL are shown, including the embedding of CLIPS with C++-based parts of the PDE. The appropriateness of the chosen approach and of the CLIPS language for knowledge-based software engineering are discussed.

Dvorak, Jiri J.↗

NASA NTRS2012

Debris Disk Structure and Morphology as Revealed by Aggressive STIS Multi-Roll Coronagraphy: A New Look at Some Old Friends

We present new imaging results from a well-selected sample of II circumstellar debris disks, all with HST pedigree, using STIS visible-light 6-roll PSF-template subtracted coronagraphy (PSFTSC). These new observations, pushing HST to its highest levels of coronagraphic performance, simultaneously probe both the interior regions of these debris systems, with inner working distances < app 8 AU for half the stars in this sample (corresponding to the giant planet and Kuiper belt regions within our own solar system), and the exterior regions far beyond. These new images enable direct inter-comparison of the architectures of these exoplanetary debris systems in the context of our own Solar System: These observations also permit us, for the first time, to characterize material in these regions at high spatial resolution and identify disk sub-structures that are signposts of planet formation and evolution; in particular, asymmetries and non-uniform debris structures that signal the presence of co-orbiting perturbing planets, and dynamical interactions (e.g., resulting in posited small grain stripping and disk "pollution") with the ISM. We focus here on recently acquired and reduced images of he circumstellar debris systems about: AU Mic (edge-on, and @ 10 pc the closest star in our sample), HD 61005, HD 32297 and HD 15115 (all with morphologies strongly suggestive of ISM wind interactions), HD 181327 & HDI07146 (close to face-on with respectively narrow and broad debris rings), and MP Mus (a "mature" proto-planetary disk hosted by a cTTS). All of our objects were previously observed in the near-IR with inferior spatial resolution and imaging efficacy, but with NICMOS r = 0.3" inner working angle (IWA) comparable to STIS multi-roll coronagraphy. The combination of new optical and existing near-IR imaging can strongly constrain the dust properties, thus enabling an assessment of grain processing and planetesimal populations. These results will directly inform upon the posited planet formation mechanisms that occur after the approximately 10 My epoch of gas depletion, a time in our solar system when giant planets were migrating and terrestrial planets were forming, and directly test theoretical models of these processes. These observations lmiquely probe both into the interior regions of these systems and are sensitive to and spatially resolve low surface-brightness (SB) material at large stellocentric distances with spatial resolution comparable to ACS and with augmenting NICMOS near-IR disk photometry in hand.

Grady, Carol A↗