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Results for “structural complexity”

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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Abstract Motivation Proteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery. Results In this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures. Availability and implementation The source code, data, and pre-trained models are available at https://github.com/jianlin-cheng/DProQA.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2008

Evaluation of Lightning Incidence to Elements of a Complex Structure: A Monte Carlo Approach

There are complex structures for which the installation and positioning of the lightning protection system (LPS) cannot be done using the lightning protection standard guidelines. As a result, there are some "unprotected" or "exposed" areas. In an effort to quantify the lightning threat to these areas, a Monte Carlo statistical tool has been developed. This statistical tool uses two random number generators: a uniform distribution to generate origins of downward propagating leaders and a lognormal distribution to generate returns stroke peak currents. Downward leaders propagate vertically downward and their striking distances are defined by the polarity and peak current. Following the electrogeometrical concept, we assume that the leader attaches to the closest object within its striking distance. The statistical analysis is run for 10,000 years with an assumed ground flash density and peak current distributions, and the output of the program is the probability of direct attachment to objects of interest with its corresponding peak current distribution.

Mata, Carlos T.↗
NASA NTRS2008

Evaluation of Lightning Incidence to Elements of a Complex Structure: A Monte Carlo Approach

There are complex structures for which the installation and positioning of the lightning protection system (LPS) cannot be done using the lightning protection standard guidelines. As a result, there are some "unprotected" or "exposed" areas. In an effort to quantify the lightning threat to these areas, a Monte Carlo statistical tool has been developed. This statistical tool uses two random number generators: a uniform distribution to generate the origin of downward propagating leaders and a lognormal distribution to generate the corresponding returns stroke peak currents. Downward leaders propagate vertically downward and their striking distances are defined by the polarity and peak current. Following the electrogeometrical concept, we assume that the leader attaches to the closest object within its striking distance. The statistical analysis is run for N number of years with an assumed ground flash density and the output of the program is the probability of direct attachment to objects of interest with its corresponding peak current distribution.

Mata, Carlos T.↗
DOE OSTI2021

Inversion of dynamical Bragg intensities to complex structure factors by iterated projections. For Ultramic. 2020. ("Pico" Festschrift, May 2021)

We discuss a method for recovering complex structure factors from many simultaneously excited Bragg beam intensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. The method is based on iterated projections between structure and scattering matrices, which are related by a matrix unitary transformation, exponential, which we invert. The algorithm removes multiple-scattering perturbations from diffraction data and might be extended to other fields, including X-ray and neutron diffraction and cryo-electron microscopy. Because coherent multiple scattering involves interference between Bragg beams, the method also solves the phase problem. Unlike dynamical inversion from electron microscope images or ptychography data, the method, which starts with Bragg beam intensities, provides complex structure factors unaffected by focusing errors or resolution limitations imposed by lenses. We provide inversions from simulated data with 441 simultaneously excited Bragg beams over a range of thickness and beam energy. We discuss the retrieval of chirality information from enantiomorphs, the efficient incorporation of symmetry information using the irreducible representation of the group of structure matrices, and the effect of HOLZ lines to provide three-dimensional information.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1993

The complex structured singular value

A tutorial introduction to the complex structured singular value (mu) is presented, with an emphasis on the mathematical aspects of mu. The mu-based methods discussed here have been useful for analyzing the performance and robustness properties of linear feedback systems. Several tests for robust stability and performance with computable bounds for transfer functions and their state space realizations are compared, and a simple synthesis problem is studied. Uncertain systems are represented using linear fractional transformations which naturally unify the frequency-domain and state space methods.

Packard, A.↗
DOE OSTI2024

Forest structural complexity and ignition pattern influence simulated prescribed fire effects

Background: Forest structural characteristics, the burning environment, and the choice of ignition pattern each influence prescribed fire behaviors and resulting fire effects; however, few studies examine the influences and interactions of these factors. Understanding how interactions among these drivers can influence prescribed fire behavior and effects is crucial for executing prescribed fires that can safely and effectively meet management objectives. To analyze the interactions between the fuels complex and ignition patterns, we used FIRETEC, a three-dimensional computational fluid dynamics fire behavior model, to simulate fire behavior and effects across a range of horizontal and vertical forest structural complexities. For each forest structure, we then simulated three different prescribed fires each with a unique ignition pattern: strip-head, dot, and alternating dot. Results: Forest structural complexity and ignition pattern affected the proportions of simulated crown scorch, consumption, and damage for prescribed fires in a dry, fire-prone ecosystem. Prescribed fires in forests with complex canopy structures resulted in increased crown consumption, scorch, and damage compared to less spatially complex forests. The choice of using a strip-head ignition pattern over either a dot or alternating-dot pattern increased the degree of crown foliage scorched and damaged, though did not affect the proportion of crown consumed. We found no evidence of an interaction between forest structural complexity and ignition pattern on canopy fuel consumption, scorch, or damage. Conclusions: We found that forest structure and ignition pattern, two powerful drivers of fire behavior that forest managers can readily account for or even manipulate, can be leveraged to influence fire behavior and the resultant fire effects of prescribed fire. These simulation findings have critical implications for how managers can plan and perform forest thinning and prescribed burn treatments to meet risk management or ecological objectives.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1984

Mathematical synthesization of complex structures

A mathematical synthesization approach for rapidly modeling and analyzing complex structures comprised of hundreds or thousands of repeating individual structural members, interconnecting hardware, and other components was described. The techniques are applicable to any structure with repeating structural members. The capabilities are embodied within the Interactive Design and Evaluation of Advanced Spacecraft (IDEAS) computer-aided design system. IDEAS has a full range of integrated spacecraft modeling, design, analysis, performance, and cost estimating capabilities which include about 40 technical program and executive, data base, and file management systems. With IDEAS, a single user at an interactive terminal can create, design, analyze, and conduct parametric studies of Earth orbiting spacecraft in a timely, cost-efficient manner. The system is particularly useful in the conceptual design phases of advanced space missions when a multiplicity of concepts must be evaluated. The IDEAS interactive finite-element modeling capabilities are discussed. The mathematical synthesization programs were structured not only to provide a detailed finite-element model of the structure but also to automatically perform the many auxiliary computations needed to analyze the spacecraft in its orbital operational environment.

Garrett, L. B.↗
DOE OSTI2024

Structural complexity of snapshots of two-dimensional Fermi-Hubbard systems

The development of quantum gas microscopy for two-dimensional optical lattices has provided an unparalleled tool to study the Fermi-Hubbard model (FHM) with ultracold atoms. Spin-resolved projective measurements, or snapshots, have played a significant role in quantifying correlation functions, theory verification, and thus the uncovering of underlying physical phenomena such as antiferromagnetism at commensurate filling on bipartite lattices and other charge and spin correlations, as well as dynamical properties at various densities. Here we employ a recent concept, the multiscale structural complexity, and show that when computed for the snapshots (of single spin species, local moments, or total density) it can provide a theory-free property, immediately accessible to experiments. Specifically, after benchmarking results for Ising and $XY$ models, we study the structural complexity of snapshots of the repulsive FHM in the two-dimensional square lattice as a function of doping and temperature. We generate projective measurements using determinant quantum Monte Carlo and compare their complexities against those from the experiment. We demonstrate that these complexities are linked to relevant physical observables such as the entropy and double occupancy. Their behaviors capture the development of correlations and relevant length scales in the system. Furthermore, we provide an open-source code in python which can be implemented into data analysis routines in experimental settings for the square lattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Oklahoma structural complexity data

Zipped file contains raster data (TIF) files and thumbnail image (PNG) files associated with modeling known and predicting structural complexity (SC) for the state of Oklahoma, two SIMPA simulation files (.SIJN) and two README (.txt) files to run both the known SC and proxy SC models using the SIMPA tool, and a "Source data catalog.xlsx" file that provides information on the source data and how it was used to represent each raster Note: Metadata including processing steps can be viewed in ESRI's ArcCatalog software

raster↗
DOE OSTI2019

Atomic-resolution visualization and doping effects of complex structures in intercalated bilayer graphene

Molecules intercalating two-dimensional materials form complex structures that have been characterized primarily by spatially averaged techniques. In this work, we use aberration-corrected scanning transmission electron microscopy and density-functional-theory (DFT) calculations to study the atomic structure of bilayer graphene (BLG) and few-layer graphene (FLG) intercalated with FeC l 3 . In BLG, we discover two distinct intercalated structures that we identify as monolayer FeC l 3 and monolayer FeC l 2 . The two structures are separated by atomically sharp boundaries and induce large free-carrier densities on the order of 10 13 c m - 2 in the graphene layers. In FLG, we observe multiple FeC l 3 layers stacked in a variety of possible configurations with respect to one another. Lastly, we find that the microscope's electron beam can convert the FeC l 3 monolayer into FeOCl monolayers in a rectangular lattice. These results reveal the need for a combination of atomically resolved microscopy, spectroscopy, and DFT calculations to identify intercalated structures and study their properties.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural predictions by using both traditional sequence alignments and Foldseek-based structure alignments, ranks structural predictions through multiple complementary metrics, and refines the structural predictions via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. MULTICOM_qa ranked 3 rd among 26 CASP15 server predictors and MULTICOM_human ranked 7 th among 87 CASP15 server and human predictors. The average TM-score of the first predictions submitted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 predictions submitted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the Foldseek Structure Alignment-based Multimer structure Generation (FSAMG) method outperforms the widely used sequence alignment-based multimer structure generation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dissipative Reactions with Intermediate-Energy Beams: A Novel Approach to Populate Complex-Structure States in Rare Isotopes

A novel pathway for the formation of multiparticle-multihole excited states in rare isotopes is reported from highly energy- and momentum-dissipative inelastic-scattering events measured in reactions of an intermediate-energy beam of 38 Ca on a Be target. The negative-parity, complex-structure final states in 38 Ca are observed following the in-beam γ-ray spectroscopy of events in the 9 Be( 38 Ca, 38 Ca + γ)X reaction in which the scattered projectile loses longitudinal momentum of order Δp || = 700 MeV/c. Here, the characteristics of the observed final states are discussed and found to be consistent with the formation of excited states involving the rearrangement of multiple nucleons in a single, highly energetic projectile-target collision. Unlike the far-less-dissipative, surface-grazing reactions usually exploited for the in-beam γ-ray spectroscopy of rare isotopes, these more energetic collisions appear to offer a practical pathway to nuclear-structure studies of more complex multiparticle configurations in rare isotopes—final states conventionally thought to be out of reach with high-luminosity fast-beam-induced reactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1974

On the recognition of complex structures: Computer software using artificial intelligence applied to pattern recognition

An approach to simultaneous interpretation of objects in complex structures so as to maximize a combined utility function is presented. Results of the application of a computer software system to assign meaning to regions in a segmented image based on the principles described in this paper and on a special interactive sequential classification learning system, which is referenced, are demonstrated.

Yakimovsky, Y.↗