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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

A Global Repository for Planet-Sized Experiments and Observations

Greenland’s ice loss doubled between 1996 and 2005. Nine of the ten warmest years on record have occurred since 2000. Carbon dioxide levels in the air are at their highest in 650,000 years. Are these phenomena related, and if so, what can they tell us about the Earth’s climate in the coming years and decades? The answer will require sophisticated computer models—and a way of dealing with the data they produce. Past climate patterns can be discerned by examining variables such as temperature and precipitation records, lake sediments, tree rings, and ice cores. Projecting future regional and global climate patterns, however, requires computer models that can simulate the complex interplay between physical, chemical, and biological processes occurring in the atmosphere, ocean, and on land and sea ice. These models are extremely computationally demanding. Over the past several decades, an ongoing revolution in high-capacity, high-performance computing has accelerated climate modeling. In 1998, a 1-year simulation of global climate using a 300- kilometer grid could be run in a day. In 2002, it took 4 or 5 hours. In 2015, this same model can be run on a high-end desktop in minutes.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2001

A Winning Cast

Howmet Research Corporation was the first to commercialize an innovative cast metal technology developed at Auburn University, Auburn, Alabama. With funding assistance from NASA's Marshall Space Flight Center, Auburn University's Solidification Design Center (a NASA Commercial Space Center), developed accurate nickel-based superalloy data for casting molten metals. Through a contract agreement, Howmet used the data to develop computer model predictions of molten metals and molding materials in cast metal manufacturing. Howmet Metal Mold (HMM), part of Howmet Corporation Specialty Products, of Whitehall, Michigan, utilizes metal molds to manufacture net shape castings in various alloys and amorphous metal (metallic glass). By implementing the thermophysical property data from by Auburn researchers, Howmet employs its newly developed computer model predictions to offer customers high-quality, low-cost, products with significantly improved mechanical properties. Components fabricated with this new process replace components originally made from forgings or billet. Compared with products manufactured through traditional casting methods, Howmet's computer-modeled castings come out on top.

Source record↗
DOE OSTI2012

Experimental Studies of NGNP Reactor Cavity Cooling System With Water

This project will investigate the flow behavior that can occur in the reactor cavity cooling system (RCCS) with water coolant under the passive cooling-mode of operation. The team will conduct separate-effects tests and develop associated scaling analyses, and provide system-level phenomenological and computational models that describe key flow phenomena during RCCS operation, from forced to natural circulation, single-phase flow and two-phase flow and flashing. The project consists of the following tasks: Task 1. Conduct separate-effects, single-phase flow experiments and develop scaling analyses for comparison to system-level computational modeling for the RCCS standpipe design. A transition from forced to natural convection cooling occurs in the standpipe under accident conditions. These tests will measure global flow behavior and local flow velocities, as well as develop instrumentation for use in larger scale tests, thereby providing proper flow distribution among standpipes for decay heat removal. Task 2. Conduct separate-effects experiments for the RCCS standpipe design as two-phase flashing occurs and flow develops. As natural circulation cooling continues without an ultimate heat sink, water within the system will heat to temperatures approaching saturation , at which point two-phase flashing and flow will begin. The focus is to develop a phenomenological model from these tests that will describe the flashing and flow stability phenomena. In addition, one could determine the efficiency of phase separation in the RCCS storage tank as the two-phase flashing phenomena ensues and the storage tank vents the steam produced. Task 3. Develop a system-level computational model that will describe the overall RCCS behavior as it transitions from forced flow to natural circulation and eventual two-phase flow in the passive cooling-mode of operation. This modeling can then be used to test the phenomenological models developed as a function of scale.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
NASA NTRS2020

Thoracic Pressure Does Not Impact CSF Pressure via Compartment Compliance

Space acquired neuro-ocular syndrome (SANS) remains a difficult risk to characterize due to the complex multi-factorial etiology related to physiological responses to the spaceflight environment. Fluid shift and the resultant change on the Cardiovascular (CV) and cerebral spinal fluid systems (CSF) in the absence of gravity continue to be considered a contributing factor to the progression of SANS. In this study, we utilize a computational model of the CSF and CV interface to establish the sensitivity that intracranial pressure, and subsequently the optic nerve sheath pressure, exhibits due to variations in thoracic pressure, assuming the cranial perfusion pressure, i.e. mean arterial pressure (MAP) to central venous pressure (CVP), is known. Methods: The GRC Cross cutting computational modeling project created as model of the CSF and CV interaction within the cranial vault by extending the work of Stevens et al. [1] by modifying the representative anatomy to include a separate venous sinus, jugular veins, secondary veins and extra jugular pathways [2-3] to more adequately represent the vascular drainage pathways from the cranial vault (Figure 1). Assuming the MAP, CVP and thoracic pressure are known, we initiated this enhanced computational model assuming a supine positon and utilized a linear ramp to vary the thoracic pressure from the assumed supine state to the target pressure corresponding to set MAP and CVP values. The model generates the time based CSF pressure values (Figure2). Results and Conclusions: Following this analysis, CSF pressure shows significant independence from thoracic pressure changes (16 mmHg in thoracic pressure produces < 1mmHg change in CSF pressure), being mostly dependent on perfusion pressure. Similarly fluid redistribution is not predicted to be impacted over a level of 1mL. We note that this simulation represents an acute changes (order of 10's of minutes) and does not represent the long term effects.

Munster, Drayton W.↗
DOE OSTI2018

The multi-assumption architecture and testbed (MAAT v1.0): R code for generating ensembles with dynamic model structure and analysis of epistemic uncertainty from multiple sources

Abstract. Here, computer models are ubiquitous tools used to represent systems across many scientific and engineering domains. For any given system, many computer models exist, each built on different assumptions and demonstrating variability in the ways in which these systems can be represented. This variability is known as epistemic uncertainty, i.e. uncertainty in our knowledge of how these systems operate. Two primary sources of epistemic uncertainty are (1) uncertain parameter values and (2) uncertain mathematical representations of the processes that comprise the system. Many formal methods exist to analyse parameter-based epistemic uncertainty, while process-representation-based epistemic uncertainty is often analysed post hoc, incompletely, informally, or is ignored. In this model description paper we present the multi-assumption architecture and testbed (MAAT v1.0) designed to formally and completely analyse process-representation-based epistemic uncertainty. MAAT is a modular modelling code that can simply and efficiently vary model structure (process representation), allowing for the generation and running of large model ensembles that vary in process representation, parameters, parameter values, and environmental conditions during a single execution of the code. MAAT v1.0 approaches epistemic uncertainty through sensitivity analysis, assigning variability in model output to processes (process representation and parameters) or to individual parameters. In this model description paper we describe MAAT and, by using a simple groundwater model example, verify that the sensitivity analysis algorithms have been correctly implemented. The main system model currently coded in MAAT is a unified, leaf-scale enzyme kinetic model of C 3 photosynthesis. In the Appendix we describe the photosynthesis model and the unification of multiple representations of photosynthetic processes. The numerical solution to leaf-scale photosynthesis is verified and examples of process variability in temperature response functions are provided. For rapid application to new systems, the MAAT algorithms for efficient variation of model structure and sensitivity analysis are agnostic of the specific system model employed. Therefore MAAT provides a tool for the development of novel or toy models in many domains, i.e. not only photosynthesis, facilitating rapid informal and formal comparison of alternative modelling approaches.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1999

Computer Aided Modeling to Determine the Effectiveness of Resistive Exercises as Countermeasures for Bone Mineral Density Loss

Due to the loss of gravitational loading, astronauts have a tendency to lose bone mineral density in their lumbar spine and lower extremities on orbit. NASA requires astronauts to perform exercises during space flight to help reduce the amount of demineralization. To test these exercises on earth, 17 week bed rest studies are conducted that consist of specific diet and exercise regimes. Developing a finite element model of these exercises will help to quantify the stress distribution imposed by of each of these exercises. To help develop this model, MRI images are acquired from individuals participating in the bed rest studies. The MRIs can be used to create a subject specific model of each individual for testing. The MRIs are processed in the Magnetic Resonance Imaging Data Transfer System program to develop a three-dimensional finite element model of the femur for evaluation. Modifications were made to the MRIDTS that simplified the model creation process. These modifications made it possible to construct two separate models of different portions of a bone simultaneously and then later connect them manually. This helped alleviate the warping problem associated with the drastic changes in geometry found in some body parts, such as the joints. The code was also modified to incorporate material properties of various bone components into the model. Interior meshing was also incorporated into the program to allow for both the cortical shell and the entire bone to be modeled. A prototype model of the right femur of an adult female is being constructed and tested to determine the feasibility of finite element analysis as a tool for evaluating exercise effectiveness. The model is being run through the ANSYS finite element program on the Alabama Super Computer Network. After the model is validated, models of bedrest subjects can be generated to investigate exercise countermeasures.

Murphy, Benjamin M.↗
NASA NTRS1986

Computer-Aided Modeling and Analysis of Power Processing Systems (CAMAPPS), phase 1

The large-signal behaviors of a regulator depend largely on the type of power circuit topology and control. Thus, for maximum flexibility, it is best to develop models for each functional block a independent modules. A regulator can then be configured by collecting appropriate pre-defined modules for each functional block. In order to complete the component model generation for a comprehensive spacecraft power system, the following modules were developed: solar array switching unit and control; shunt regulators; and battery discharger. The capability of each module is demonstrated using a simplified Direct Energy Transfer (DET) system. Large-signal behaviors of solar array power systems were analyzed. Stability of the solar array system operating points with a nonlinear load is analyzed. The state-plane analysis illustrates trajectories of the system operating point under various conditions. Stability and transient responses of the system operating near the solar array's maximum power point are also analyzed. The solar array system mode of operation is described using the DET spacecraft power system. The DET system is simulated for various operating conditions. Transfer of the software program CAMAPPS (Computer Aided Modeling and Analysis of Power Processing Systems) to NASA/GSFC (Goddard Space Flight Center) was accomplished.

Kim, S.↗
NASA NTRS1975

Technical description of space ultra reliable modular computer (SUMC), model 2 B

The design features of the SUMC-2B computer, also called the IBM-HTC are described. It is general purpose digital computer implemented with flexible hardware elements and microprograming to enable low cost customizing to a wide range of applications. It executes the S/360 standard instruction set to maintain problem state compability. Memory technology, extended instruction sets, and I/O channel variations are among the available options.

Source record↗
NASA NTRS2012

CFD Assessment of Forward Booster Separation Motor Ignition Overpressure on ET XT 718 Ice/Frost Ramp

Computational fluid dynamics assessment of the forward booster separation motor ignition over-pressure was performed on the space shuttle external tank X(sub T) 718 ice/frost ramp using the flow solver OVERFLOW. The main objective of this study was the investigation of the over-pressure during solid rocket booster separation and its affect on the local pressure and air-load environments. Delta pressure and plume impingement were investigated as a possible contributing factor to the cause of the debris loss on shuttle missions STS-125 and STS-127. A simplified computational model of the Space Shuttle Launch Vehicle was developed consisting of just the external tank and the solid rocket boosters with separation motor nozzles and plumes. The simplified model was validated by comparison to full fidelity computational model of the Space Shuttle without the separation motors. Quasi steady-state plume solutions were used to calibrate the thrust of the separation motors. Time-accurate simulations of the firing of the booster-separation motors were performed. Parametric studies of the time-step size and the number of sub-iterations were used to find the best converged solution. The computed solutions were compared to previous OVERFLOW steady-state runs of the separation motors with reaction control system jets and to ground test data. The results indicated that delta pressure from the overpressure was small and within design limits, and thus was unlikely to have contributed to the foam losses.

Tejnil, Edward↗
NASA NTRS1995

Parametrics on 2D Navier-Stokes analysis of a Mach 2.68 bifurcated rectangular mixed-compression inlet

The supersonic diffuser of a Mach 2.68 bifurcated, rectangular, mixed-compression inlet was analyzed using a two-dimensional (2D) Navier-Stokes flow solver. Parametric studies were performed on turbulence models, computational grids and bleed models. The computer flowfield was substantially different from the original inviscid design, due to interactions of shocks, boundary layers, and bleed. Good agreement with experimental data was obtained in many aspects. Many of the discrepancies were thought to originate primarily from 3D effects. Therefore, a balance should be struck between expending resources on a high fidelity 2D simulation, and the inherent limitations of 2D analysis. The solutions were fairly insensitive to turbulence models, grids and bleed models. Overall, the k-e turbulence model, and the bleed models based on unchoked bleed hole discharge coefficients or uniform velocity are recommended. The 2D Navier-Stokes methods appear to be a useful tool for the design and analysis of supersonic inlets, by providing a higher fidelity simulation of the inlet flowfield than inviscid methods, in a reasonable turnaround time.

Mizukami, M.↗
NASA NTRS1998

Flow and Turbulence Modeling and Computation of Shock Buffet Onset for Conventional and Supercritical Airfoils

Flow and turbulence models applied to the problem of shock buffet onset are studied. The accuracy of the interactive boundary layer and the thin-layer Navier-Stokes equations solved with recent upwind techniques using similar transport field equation turbulence models is assessed for standard steady test cases, including conditions having significant shock separation. The two methods are found to compare well in the shock buffet onset region of a supercritical airfoil that involves strong trailing-edge separation. A computational analysis using the interactive-boundary layer has revealed a Reynolds scaling effect in the shock buffet onset of the supercritical airfoil, which compares well with experiment. The methods are next applied to a conventional airfoil. Steady shock-separated computations of the conventional airfoil with the two methods compare well with experiment. Although the interactive boundary layer computations in the shock buffet region compare well with experiment for the conventional airfoil, the thin-layer Navier-Stokes computations do not. These findings are discussed in connection with possible mechanisms important in the onset of shock buffet and the constraints imposed by current numerical modeling techniques.

Bartels, Robert E.↗
NASA NTRS1972

Integration methods where force is obtained from the smoothed gravitational field.

Discussion of the application of computer models to collisionless stellar systems. Two more recent computer models - i.e., the two-dimensional rod model, and the model for disks of stars - are described. It is shown that the dynamics of collisionless stellar systems can be studied by representing the system by large numbers of representative stars.

Hohl, F.↗
NASA NTRS1991

The formation of antipodal-impact terrains on Mars

The regions antipodal to Mars' three largest impact basins, Hellas, Isidis, and Argyre, were assessed for evidence of impact induced seismically disrupted terrains. Photogeology and preliminary computer modeling using the Simplified Arbitrary Lagrangian-Eulerian computer program suggest such terrain could have been formed by the Hellas and Isidis impacts. Previously, the only assessment of potential surface disruptions on Mars antipodal to large impacts was by Peterson (1978). Herein, the results give credence to Peterson's assertions. For Hellas, the computer model clearly suggests that antipodal pressures were probably strong enough to have fractured the crust and disrupted the surface, and may account for aspects of volcanism at Alba Patera. It is suggested that the Hellas impact produced sufficient focused energy at its antipode to produce deep fracture in the Martian crust centered below the current caldera for Alba Petera. With the generation and evolution of magma in the Tharsis area, the fracture system provided a ready conduit for early stage eruptions of Martians lavas derived from deep in the crust and/or upper mantle, perhaps of komatiitic composition.

Williams, D. A.↗
NASA NTRS1994

Instructable autonomous agents

In contrast to current intelligent systems, which must be laboriously programmed for each task they are meant to perform, instructable agents can be taught new tasks and associated knowledge. This thesis presents a general theory of learning from tutorial instruction and its use to produce an instructable agent. Tutorial instruction is a particularly powerful form of instruction, because it allows the instructor to communicate whatever kind of knowledge a student needs at whatever point it is needed. To exploit this broad flexibility, however, a tutorable agent must support a full range of interaction with its instructor to learn a full range of knowledge. Thus, unlike most machine learning tasks, which target deep learning of a single kind of knowledge from a single kind of input, tutorability requires a breadth of learning from a broad range of instructional interactions. The theory of learning from tutorial instruction presented here has two parts. First, a computational model of an intelligent agent, the problem space computational model, indicates the types of knowledge that determine an agent's performance, and thus, that should be acquirable via instruction. Second, a learning technique, called situated explanation specifies how the agent learns general knowledge from instruction. The theory is embodied by an implemented agent, Instructo-Soar, built within the Soar architecture. Instructo-Soar is able to learn hierarchies of completely new tasks, to extend task knowledge to apply in new situations, and in fact to acquire every type of knowledge it uses during task performance - control knowledge, knowledge of operators' effects, state inferences, etc. - from interactive natural language instructions. This variety of learning occurs by applying the situated explanation technique to a variety of instructional interactions involving a variety of types of instructions (commands, statements, conditionals, etc.). By taking seriously the requirements of flexible tutorial instruction, Instructo-Soar demonstrates a breadth of interaction and learning capabilities that goes beyond previous instructable systems, such as learning apprentice systems. Instructo-Soar's techniques could form the basis for future 'instructable technologies' that come equipped with basic capabilities, and can be taught by novice users to perform any number of desired tasks.

Huffman, Scott Bradley↗
NASA NTRS1949

Some New Problems on Shells and Thin Structures

Cylindrical shells of arbitrary section, reinforced by longitudinal and transverse members (stringers and ribs) are considered by us, for a sufficiently close spacing of the ribs, as in our previously published papers (references 1 end 2), as thin-walled orthotropic spatial systems at the cross-sections of which only axial (normal and shearing) forces can arise. The longitudinal bending and twisting moments, due to their weak effect on the stress state of the shell, are taken equal to zero. Along the longitudinal sections of the shell there may arise transverse forces in addition to the normal ~d shearing forces. Under the so-called static assumptions there is taken for the computation model of the shell a thin-walled spatial system consisting along its length (along a generator) of an infinite number of elementary strips capable of bending. Each of these strips is likened to a curved rod operating in each of its sections not only in tension (compression)but also in transverse bending and shear. The interaction between two adjoining transverse strips in the shell expresses itself in the transmission from one strip to the other of only the normal and shearing stresses. The static structure of the computation model here described is shown in figure 1, where the connections through which the normal and shearing stresses transmitted from one transverse strip to smother are indicated schematically by the rods located in the middle surface of the shell. In addition to the static hypothesis we introduce also geometric hypotheses. According to the latter the elongational deformations of the shell along lines parallel to the generator of its middle surface and the shear deformations in the middle surface, as ma+gitudes having . little effect on the state of the fundamental internal forces of the shell, are taken equal to zero. The deformations of the shell in our computational model are such that in the first place the lines of this surface perpendicular to the generator are inextensible at each point end in the second place the angles between the lines of principal curvature (the coordinate lines) which are straight before the deformation remain straight after the deformation.

Vlasov, V. S.↗
DOE OSTI2013

System-based identification of toxicity pathways associated with multi-walled carbon nanotube-induced pathological responses

The fibrous shape and biopersistence of multi-walled carbon nanotubes (MWCNT) have raised concern over their potential toxicity after pulmonary exposure. As in vivo exposure to MWCNT produced a transient inflammatory and progressive fibrotic response, this study sought to identify significant biological processes associated with lung inflammation and fibrosis pathology data, based upon whole genome mRNA expression, bronchoaveolar lavage scores, and morphometric analysis from C57BL/6J mice exposed by pharyngeal aspiration to 0, 10, 20, 40, or 80 μg MWCNT at 1, 7, 28, or 56 days post-exposure. Using a novel computational model employing non-negative matrix factorization and Monte Carlo Markov Chain simulation, significant biological processes with expression similar to MWCNT-induced lung inflammation and fibrosis pathology data in mice were identified. A subset of genes in these processes was determined to be functionally related to either fibrosis or inflammation by Ingenuity Pathway Analysis and was used to determine potential significant signaling cascades. Two genes determined to be functionally related to inflammation and fibrosis, vascular endothelial growth factor A (vegfa) and C-C motif chemokine 2 (ccl2), were confirmed by in vitro studies of mRNA and protein expression in small airway epithelial cells exposed to MWCNT as concordant with in vivo expression. This study identified that the novel computational model was sufficient to determine biological processes strongly associated with the pathology of lung inflammation and fibrosis and could identify potential toxicity signaling pathways and mechanisms of MWCNT exposure which could be used for future animal studies to support human risk assessment and intervention efforts. - Highlights: • A novel computational model identified toxicity pathways matching in vivo pathology. • Systematic identification of MWCNT-induced biological processes in mouse lungs • MWCNT-induced functional networks of lung inflammation and fibrosis were revealed. • Two functional, representative genes, ccl2 and vegfa, were validated in vitro.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

V&V Framework

A Verification and Validation (V&V) framework is presented for the development and execution of coordinated modeling and experimental program s to assess the predictive capability of computational models of complex systems through focused, well structured, and formal processes. The elements of the framework are based on established V&V methodology developed by various organizations including the Department of Energy, National Aeronautics and Space Administration, the American Institute of Aeronautics and Astronautics, and the American Society of Mechanical Engineers. Four main topics are addressed: 1) Program planning based on expert elicitation of the modeling physics requirements, 2) experimental design for model assessment, 3) uncertainty quantification for experimental observations and computational model simulations, and 4) assessment of the model predictive capability. The audience for this document includes program planners, modelers, experimentalist, V &V specialist, and customers of the modeling results.

97 MATHEMATICS AND COMPUTING↗