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Results for “integrative structural modeling”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS1977

Structural model integrity

Many of the practical aspects and problems of ensuring the integrity of a structural model are discussed, as well as the steps which have been taken in the NASTRAN system to assure that these checks can be routinely performed. Model integrity as used applies not only to the structural model but also to the loads applied to the model. Emphasis is also placed on the fact that when dealing with substructure analysis, all of the checking procedures discussed should be applied at the lowest level of substructure prior to any coupling.

Wallerstein, D. V.↗
DOE OSTI2025

Integrated structural model of the palladin–actin complex using XL ‐ MS , docking, NMR , and SAXS

Abstract Palladin is an actin‐binding protein that accelerates actin polymerization and is linked to the metastasis of several types of cancer. Previously, three lysine residues in an immunoglobulin‐like domain of palladin have been identified as essential for actin binding. However, it is still unknown where palladin binds to F‐actin. Evidence that palladin binds to the sides of actin filaments to facilitate branching is supported by our previous study showing that palladin was able to compensate for Arp2/3 in the formation of Listeria actin comet tails. Here, we used chemical crosslinking to covalently link palladin and F‐actin residues based on spatial proximity. Samples were then enzymatically digested, separated by liquid chromatography, and analyzed by tandem mass spectrometry. Peptides containing the crosslinks and specific residues involved were then identified for input to the HADDOCK docking server to model the most likely binding conformation. Small‐angle x‐ray scattering was used to provide further insight into palladin flexibility and the binding interface, and NMR spectra identified potential interactions between palladin's Ig domains. Our final structural model of the F‐actin:palladin complex revealed how palladin interacts with and stabilizes F‐actin at the interface between two actin monomers. Three actin residues that were identified in this study also appear commonly in the actin‐binding interface with other proteins such as myotilin, myosin, and tropomodulin. An accurate structural representation of the complex between palladin and actin extends our understanding of palladin's role in promoting cancer metastasis through the regulation of actin dynamics.

Sargent, Rachel [Department of Chemistry and Bioch↗
DOE OSTI2023

3D-equivariant graph neural networks for protein model quality assessment

Quality assessment (QA) of predicted protein tertiary structure models plays an important role in ranking and using them. With the recent development of deep learning end-to-end protein structure prediction techniques for generating highly confident tertiary structures for most proteins, it is important to explore corresponding QA strategies to evaluate and select the structural models predicted by them since these models have better quality and different properties than the models predicted by traditional tertiary structure prediction methods. We develop EnQA, a novel graph-based 3D-equivariant neural network method that is equivariant to rotation and translation of 3D objects to estimate the accuracy of protein structural models by leveraging the structural features acquired from the state-of-the-art tertiary structure prediction method—AlphaFold2. We train and test the method on both traditional model datasets (e.g. the datasets of the Critical Assessment of Techniques for Protein Structure Prediction) and a new dataset of high-quality structural models predicted only by AlphaFold2 for the proteins whose experimental structures were released recently. Our approach achieves state-of-the-art performance on protein structural models predicted by both traditional protein structure prediction methods and the latest end-to-end deep learning method—AlphaFold2. It performs even better than the model QA scores provided by AlphaFold2 itself. The results illustrate that the 3D-equivariant graph neural network is a promising approach to the evaluation of protein structural models. Integrating AlphaFold2 features with other complementary sequence and structural features is important for improving protein model QA.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

Integrated Modeling Methodology Validation Using the Micro-Precision Interferometer Testbed

This paper validates the integrated modeling methodology used for design and performance evaluation of complex opto-mechanical systems, particularly spaceborne interferometers. The methodology integrates structural modeling, optical modeling, and control system design into a common environment, the Integrated Modeling of Optical Systems (IMOS) software package.

opto-mechanical↗
NASA NTRS1989

Methodology for analysis and simulation of large multidisciplinary problems

The Integrated Structural Modeling (ISM) program is being developed for the Air Force Weapons Laboratory and will be available for Air Force work. Its goal is to provide a design, analysis, and simulation tool intended primarily for directed energy weapons (DEW), kinetic energy weapons (KEW), and surveillance applications. The code is designed to run on DEC (VMS and UNIX), IRIS, Alliant, and Cray hosts. Several technical disciplines are included in ISM, namely structures, controls, optics, thermal, and dynamics. Four topics from the broad ISM goal are discussed. The first is project configuration management and includes two major areas: the software and database arrangement and the system model control. The second is interdisciplinary data transfer and refers to exchange of data between various disciplines such as structures and thermal. Third is a discussion of the integration of component models into one system model, i.e., multiple discipline model synthesis. Last is a presentation of work on a distributed processing computing environment.

Russell, William C.↗
NASA NTRS1992

Glass sample preparation and performance investigations

This final report details the work performed under this delivery order from April 1991 through April 1992. The currently available capabilities for integrated optical performance modeling at MSFC for large and complex systems such as AXAF were investigated. The Integrated Structural Modeling (ISM) program developed by Boeing for the U.S. Air Force was obtained and installed on two DECstations 5000 at MSFC. The structural, thermal and optical analysis programs available in ISM were evaluated. As part of the optomechanical engineering activities, technical support was provided in the design of support structure, mirror assembly, filter wheel assembly and material selection for the Solar X-ray Imager (SXI) program. As part of the fabrication activities, a large number of zerodur glass samples were prepared in different sizes and shapes for acid etching, coating and polishing experiments to characterize the subsurface damage and stresses produced by the grinding and polishing operations. Various optical components for AXAF video microscope and the x-ray test facility were also fabricated. A number of glass fabrication and test instruments such as a scatter plate interferometer, a gravity feed saw and some phenolic cutting blades were fabricated, integrated and tested.

Johnson, R. Barry↗
NASA NTRS1985

High Reynolds number tests of a NASA SC(3)-0712(B) airfoil in the Langley 0.3-meter transonic cryogenic tunnel

A wind tunnel investigation of a NASA 12-percent-thick, advanced-technology supercritical airfoil was conducted in the Langley 0.3-Meter Transonic Cryogenic Tunnel (TCT). This investigation represents another in the series of NASA/U.S. industry two-dimensional airfoil studies to be completed in the Advanced Technology Airfoil Tests program. Test temperature was varied from 220 K to 96 K at pressures ranging from 1.2 to 4.3 atm. Mach number was varied from 0.60 to 0.80. These variables provided a Reynolds number range from 4,400,000 to 40,000,000 based on a 15.24-cm (6.0-in.) airfoil chord. This investigation was designed to test a NASA advanced-technology airfoil from low to flight-equivalent Reynolds numbers, provide experience in cryogenic wind tunnel model design and testing techniques, and demonstrate the suitability of the 0.3-m TCT as an airfoil test facility. The aerodynamic results are presented as integrated force and moment coefficients and pressure distributions. Data are included which demonstrate the effects of fixed transition, Mach number, and Reynolds number on the aerodynamic characteristics. Also included are remarks on the model design, the model structural integrity, and the overall test experience.

Johnson, W. G., Jr.↗
DOE OSTI2022

Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair

The xeroderma pigmentosum protein A (XPA) and replication protein A (RPA) proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair (NER) pathway. We have previously characterized the two interaction sites, one between the XPA N-terminal (XPA-N) disordered domain and the RPA32 C-terminal domain (RPA32C), and the other with the XPA DNA binding domain (DBD) and the RPA70AB DBDs. Here, we show that XPA mutations that inhibit the physical interaction in either site reduce NER activity in biochemical and cellular systems. Combining mutations in the two sites leads to an additive inhibition of NER, implying that they fulfill distinct roles. Our data suggest a model in which the interaction between XPA-N and RPA32C is important for the initial association of XPA with NER complexes, while the interaction between XPA DBD and RPA70AB is needed for structural organization of the complex to license the dual incision reaction. Integrative structural models of complexes of XPA and RPA bound to single-stranded/double-stranded DNA (ss/dsDNA) junction substrates that mimic the NER bubble reveal key features of the architecture of XPA and RPA in the preincision complex. Most critical among these is that the shape of the NER bubble is far from colinear as depicted in current models, but rather the two strands of unwound DNA must assume a U-shape with the two ss/dsDNA junctions localized in close proximity. Our data suggest that the interaction between XPA and RPA70 is key for the organization of the NER preincision complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Integration of software tools for integrative modeling of biomolecular systems

Integrative modeling computes a model based on varied types of input information, be it from experiments or prior models. Often, a type of input information will be best handled by a specific modeling software package. In such a case, we desire to integrate our integrative modeling software package, Integrative Modeling Platform (IMP), with software specialized to the computational demands of the modeling problem at hand. After several attempts, however, we have concluded that even in collaboration with the software's developers, integration is either impractical or impossible. The reasons for the intractability of integration include software incompatibilities, differing modeling logic, the costs of collaboration, and academic incentives. In the integrative modeling software ecosystem, several large modeling packages exist with often redundant tools. So we reason, therefore, that the other development groups have similarly concluded that the benefit of integration does not justify the cost. As a result, modelers are often restricted to the set of tools within a single software package. The inability to integrate tools from distinct software negatively impacts the quality of the models and the efficiency of the modeling. As the complexity of modeling problems grows, we seek to galvanize developers and modelers to consider the long-term benefit that software interoperability yields. In this article, we formulate a demonstrative set of software standards for implementing a model search using tools from independent software packages and discuss our efforts to integrate IMP and the crystallography suite Phenix within the Bayesian modeling framework.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Membrane Options for IER 296 TEX-MOX [Slides]

This set of slides summarizes the structural analysis progress related to the LANL design engineering effort for the IER 296 Critical Experiment. FEA simulation results are presented for the determination of the membrane material and thickness to be used based on a combination of factors such as metal purity, deflection, and structural integrity. Model geometry uses Planet Top Plate described in LANL drawing 128Y271039-D11 and generic adapter plate like that described in LANL drawing 128Y1721030.

42 ENGINEERING↗
DOE OSTI2021

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current ‘state of the art’ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of ‘soft recommendations’ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage ‘open science’ practices.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1982

High Reynolds number tests of a Boeing BAC I airfoil in the Langley 0.3-meter transonic cryogenic tunnel

A wind tunnel investigation of an advanced-technology airfoil was conducted in the Langley 0.3-Meter Transonic Cryogenic Tunnel (TCT). This investigation represents the first in a series of NASA/U.X. industry two dimensional airfoil studies to be completed in the Advanced Technology Airfoil Test program. Test temperature was varied from ambient to about 100 K at pressures ranging from about 1.2 to 6.0 atm. Mach number was varied from about 0.40 to 0.80. These variables provided a Reynolds number (based on airfoil chord) range from about .0000044 to .00005. This investigation was specifically designed to: (1) test a Boeing advanced airfoil from low to flight-equivalent Reynolds numbers; (2) provide the industry participant (Boeing) with experience in cryogenic wind-tunnel model design and testing techniques; and (3) demonstrate the suitability of the 0.3-m TCT as an airfoil test facility. All the objectives of the cooperative test were met. Data are included which demonstrate the effects of fixed transition, Mach number, and Reynolds number on the aerodynamic characteristics of the airfoil. Also included are remarks on the model design, the model structural integrity, and the overall test experience.

Johnson, W. G., Jr.↗
NASA NTRS1985

Pressure distributions from high Reynolds number tests of a Boeing BAC 1 airfoil in the Langley 0.3-meter transonic cryogenic tunnel

A wind-tunnel investigation designed to test a Boeing advanced-technology airfoil from low to flight-equivalent Reynolds numbers has been completed in the Langley 0.3-Meter Transonic Cryogenic Tunnel. This investigation represents the first in a series of NASA/U.S. industry two-dimensional airfoil studies to be completed in the Advanced Technology Airfoil Test program. Test temperature was varied from ambient to about 100 K at pressures ranging from about 1.2 to 6.0 atm. Mach number was varied from about 0.40 to 0.80. These variables provided a Reynolds number (based on airfoil chord) range from 4.4 X 10 to the 6th power to 50.0 X 10 to the 6th power. All the test objectives were met. The pressure data are presented without analysis in plotted and tabulated formats for use in conjunction with the aerodynamic coefficient data published as NASA TM-81922. At the time of the test, these pressure data were considered proprietary and have only recently been made available by Boeing for general release. Data are included which demonstrate the effects of fixed transition. Also included are remarks on the model design, the model structural integrity, and the overall test experience.

Johnson, W. G., Jr.↗
NASA NTRS1986

High Reynolds number tests of a Douglas DLBA 032 airfoil in the Langley 0.3-meter transonic cryogenic tunnel

A wind-tunnel investigation of a Douglas advanced-technology airfoil was conducted in the Langley 0.3-Meter Transonic Cryogenic Tunnel (0.3-m TCT). The temperature was varied from 227 K (409 R) to 100 K (180 R) at pressures ranging from about 159 kPa (1.57 atm) to about 514 kPa (5.07 atm). Mach number was varied from 0.50 to 0.78. These variables provided a Reynolds number range (based on airfoil chord) from 6.0 to 30.0 x 10 to the 6th power. This investigation was specifically designed to: (1) test a Douglas airfoil from moderately low to flight-equivalent Reynolds numbers, and (2) evaluate sidewall-boundary-layer effects on transonic airfoil performance characteristics by a systematic variation of Mach number, Reynolds number, and sidewall-boundary-layer removal. Data are included which demonstrate the effects of fixing transition, Mach number, Reynolds number, and sidewall-boundary-layer removal on the aerodynamic characteristics of the airfoil. Also included are remarks on model design and model structural integrity.

Johnson, Charles B.↗
NASA NTRS1988

Control of optical systems

Some of the current and planned activities at the Air Force Systems Command in structures and controls for optical-type systems are summarized. Many of the activities are contracted to industry; one task is an in-house program which includes a hardware test program. The objective of the in-house program, referred to as the Aluminum Beam Expander Structure (ABES), is to address issues involved in on-orbit system identification. The structure, which appears similar to the LDR backup structure, is about 35 feet tall. The activity to date has been limited to acquisition of about 250 hours of test data. About 30 hours of data per excitation force is gathered in order to obtain sufficient data for a good statistical estimate of the structural parameters. The development of an Integrated Structural Modeling (ISM) computer program is being done by Boeing Aerospace Company. The objective of the contracted effort is to develop a combined optics, structures, thermal, controls, and multibody dynamics simulation code.

Founds, D.↗