Engineering Papers⌕ Search

SEARCH · Engineering Papers

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structural Complexity and Tuned Thermoelectric Properties of a Polymorph of the Zintl Phase Ca 2 CdSb 2 with a Non-centrosymmetric Monoclinic Structure

The Zintl phase Ca 2 CdSb 2 was found to be dimorphic. Besides the orthorhombic Ca 2 CdSb 2 (-o), here we report on the synthesis, the structural characterization, and the thermoelectric transport properties of its monoclinic form, Ca 2 CdSb 2 (-m), and its Lu-doped variant Ca 2–x Lu x CdSb 2 (x ≈ 0.02). The monoclinic structure exhibits complex structural characteristics and constitutes a new structure type with the non-centrosymmetric space group Cm (Z = 30). The electrical resistivity ρ(T) measured on single crystals of both phases portrays a transition from a semiconductor to a degenerate p-type semiconductor upon doping with Lu and with an attendant change in the Hall carrier concentration nH from 7.15 × 10 18 to 2.30 × 10 19 cm –3 at 300 K. The Seebeck coefficient S(T) of both phases are comparable and indicate a hole-dominated carrier transport mechanism with magnitudes of 133 and 116 μV/K at 600 K for Ca 2 CdSb 2 (-m) and Ca 2–x Lu x CdSb 2 , respectively. The convoluted atomic bonding with an attendant large unit cell volume of ~4365 Å 3 drives a putative low thermal conductivity in these materials resulting in a power factor PF of 1.63 μW/cm K 2 and an estimated thermoelectric figure of merit zT of ~0.5 for Ca 2–x Lu x CdSb 2 at 600 K. Furthermore, differential scanning calorimetry results reveal the stability of these phases up to about 960 K, making them candidates for moderate temperature thermoelectric materials.

36 MATERIALS SCIENCE↗
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↗
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↗
DOE OSTI2015

Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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↗
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 OSTI2014

Formation of less-known structurally complex ζ{sub b} and orthorhombic quasicrystalline approximant ε{sub n} on solidification of selected Al–Pd–Cr alloys

The evolution of phases was investigated on cooling of Al{sub 71}Pd{sub 24}Cr{sub 5}, Al{sub 73}Pd{sub 20}Cr{sub 7}, and Al{sub 73}Pd{sub 23}Cr{sub 4} alloys from 1350 °C down to ambient temperature with the rate of 10 °C·min{sup −1}. To perform the investigation, differential thermal analysis, synchrotron X-ray powder diffraction, and scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy were used. In all the investigated alloys structurally complex phases ε{sub n} (ε{sub 6} + ε{sub 28}) and ζ{sub b}, as well as the δ-phase were identified. Based on the results of differential thermal analysis, sequences of phase transformations were determined. The Al{sub 71}Pd{sub 24}Cr{sub 5} alloy started to solidify at 1031.4 °C through β. Primary dendrites of ζ{sub b} were observed in Al{sub 73}Pd{sub 20}Cr{sub 7} and Al{sub 73}Pd{sub 23}Cr{sub 4} alloys. In the second step of solidification δ and/or ζ{sub b} were formed. The peritectic reaction, liquid + ζ{sub b} + δ → ε{sub n} + ζ{sub b} + δ, leading to the formation of the quasicrystalline approximant ε{sub n} (ε{sub 6} + ε{sub 28}) took place in the final step of solidification at approximately 792 °C. - Highlights: • Structurally complex ε{sub n} (ε{sub 6} + ε{sub 28}), ζ{sub b} and δ-phases were identified. • The Al{sub 71}Pd{sub 24}Cr{sub 5} alloy started to solidify at 1031.4 °C through the primary β phase. • The Al{sub 73}Pd{sub 20}Cr{sub 7} and Al{sub 73}Pd{sub 23}Cr{sub 4} alloys solidified in the same way. • The quasicrystalline approximant ε{sub n} (ε{sub 6} + ε{sub 28}) was formed at approximately 792 °C.

36 MATERIALS SCIENCE↗
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 OSTI2014

The complex structure of stars in the outer galactic disk as revealed by Pan-STARRS1

We present a panoptic view of the stellar structure in the Galactic disk's outer reaches commonly known as the Monoceros Ring, based on data from Pan-STARRS1. These observations clearly show the large extent of the stellar overdensities on both sides of the Galactic disk, extending between b = –25° and b = +35° and covering over 130° in Galactic longitude. The structure exhibits a complex morphology with both stream-like features and a sharp edge to the structure in both the north and the south. We compare this map to mock observations of two published simulations aimed at explaining such structures in the outer stellar disk, one postulating an origin as a tidal stream and the other demonstrating a scenario where the disk is strongly distorted by the accretion of a satellite. These morphological comparisons of simulations can link formation scenarios to observed structures, such as demonstrating that the distorted-disk model can produce thin density features resembling tidal streams. Although neither model produces perfect agreement with the observations—the tidal stream predicts material at larger distances that is not detected while in the distorted disk model, the midplane is warped to an excessive degree—future tuning of the models to accommodate these latest data may yield better agreement.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Quantifying vegetation and canopy structural complexity from terrestrial LiDAR data using the FORESTR R package

Terrestrial LiDAR (light detection and ranging) technologies have created new means of quantifying forest canopy structure, allowing not only the estimation of biomass, but also descriptions of the position and variability in canopy elements in space. Such measures provide novel structural information broadly useful to ecologists. There is a growing need for both a detailed taxonomy of forest canopy structural complexity (CSC) and open, transparent, and flexible tools to quantify complexity in ways that will advance foundational ecological knowledge of structure-function relationships. The CSC taxonomy we present groups structural descriptors into five categories: leaf area and density, canopy height, canopy arrangement, canopy openness, and canopy variability. This paper also introduces the r package forestr, the first open-source r package for the calculation of CSC metrics from terrestrial LiDAR data. The r package forestr is an analysis toolbox that works with portable canopy LiDAR (PCL) data and other pixelated/voxelized point clouds derived from terrestrial LiDAR scanning (TLS) data to calculate CSC metrics of interest to ecologists, modellers, forest managers, and remote sensing scientists.

52 ecosystem↗
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↗
DOE OSTI2026

Stabilizing homogeneous CaMn6Sn6via oscillatory crystal growth: structural complexity in a kagome metal

CaMn6Sn6 is a member of the large family of Mn-based kagome metals derived by filling voids of the prototypical CoSn structure. We observed Ca-deficiency and structural complexity, with approximately 10% deficiency of calcium relative to the ideal 166 stoichiometry. These features are common in related Ca-based materials. We find that growth conditions stabilize different phases with varying Curie temperatures. Diffraction and magnetization measurements reveal that conventional growth profiles yield inhomogeneity both within and between crystals in a given batch, whereas an oscillatory temperature profile promotes homogeneous crystals that adopt a superstructure beyond the parent hexagonal structure type. We present the physical properties of crystals grown using the oscillatory approach. The crystals are highly conductive, with a c-axis residual resistivity ratio ρ(300 K)/ρ(2 K) exceeding 100 and a positive, linear magnetoresistance at base temperature. Magnetically, the crystals are quite similar to MgMn6Sn6, with easy-plane ferromagnetic behavior and a Curie temperature of TC ≈ 237 K. These results highlight the critical role of growth conditions in stabilizing homogeneous crystals of complex phases such as Ca0.9Mn6Sn6. The oscillatory growth approach provides an effective route for accessing the intrinsic properties of this complex material and may be broadly useful for the growth of related kagome systems.

May, Andrew [ORNL] (ORCID:0000000307778539)↗
DOE OSTI2020

A Geometric Measure Theory Approach to Identify Complex Structural Features on Soft Matter Surfaces

The structural features that protrude above or below a soft matter interface are well-known to be related to interfacially mediated chemical reactivity and transport processes. It is a challenge to develop a robust algorithm for identifying these organized surface structures, as the morphology can be highly varied and they may exist on top of an interface containing significant interfacial roughness. A new algorithm that employs concepts from geometric measure theory, algebraic topology, and optimization is developed to identify candidate structures at a soft matter surface, and then, using a probabilistic approach, to rank their likelihood of being a complex structural feature. The algorithm is tested for a surfactant laden water/oil interface, where it is robust to identifying protrusions responsible for water transport against a set identified by visual inspection. To our knowledge, this is the first example of applying geometric measure theory to analyze the properties of a chemical/materials science system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Corrigendum to "Predicting biomass of hyperdiverse and structurally complex central Amazonian forests — a virtual approach using extensive field data" Published in Biogeosciences, 13, 1553-1570, 2016

Old-growth forests are subject to substantial changes in structure and species composition due to the intensification of human activities, gradual climate change and extreme weather events. Trees store ca. 90% of the total aboveground biomass (AGB) in tropical forests and precise tree biomass estimation models are crucial for management and conservation. In the central Amazon, predicting AGB at large spatial scales is a challenging task due to the heterogeneity of successional stages, high tree species diversity and inherent variations in tree allometry and architecture. We parameterized generic AGB estimation models applicable across species and a wide range of structural and compositional variation related to species sorting into height layers as well as frequent natural disturbances. We used 727 trees (diameter at breast height ≥5 cm) from 101 genera and at least 135 species harvested in a contiguous forest near Manaus, Brazil. Sampling from this data set we assembled six scenarios designed to span existing gradients in floristic composition and size distribution in order to select models that best predict AGB at the landscape level across successional gradients. We found that good individual tree model fits do not necessarily translate into reliable predictions of AGB at the landscape level. We observed systematic biases ranging from -31% (pantropical) to +39 %, with root-mean-square error (RMSE) values of up to 130-Mg ha -1 (pantropical), when predicting AGB (dry mass) over scenarios using our different models and an available pantropical model. Our first and second best models had both low mean biases (0.8 and 3.9 %, respectively) and RMSE (9.4 and 18.6 Mg ha -1 ) when applied over scenarios. Predicting biomass correctly at the landscape level in hyperdiverse and structurally complex tropical forests, especially allowing good performance at the margins of data availability for model construction/calibration, requires the inclusion of predictors that express inherent variations in species architecture. Furthermore, the model of interest should comprise the floristic composition and size-distribution variability of the target forest, implying that even generic global or pantropical biomass estimation models can lead to strong biases. Reliable biomass assessments for the Amazon basin (i.e., secondary forests) still depend on the collection of allometric data at the local/regional scale and forest inventories including species-specific attributes, which are often unavailable or estimated imprecisely in most regions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Symmetry-specific orientational order parameters for complex structures

A comprehensive framework of characterizing complex self-assembled structures with a set of orientational order parameters is presented. It is especially relevant in the context of using anisotropic building blocks with various symmetries. Two classes of tensor order parameters are associated with polyhedral nematic and bond orientational order. For the latter, a variation of classical bond order parameters (BOPs) is introduced, which takes advantage of the symmetry of constituent particles and/or expected crystalline phases. These symmetrized BOPs can be averaged over an entire system or assigned locally to an individual bond. By combining that with the bond percolation procedure, one is able to identify coherent domains within a self-assembled structure. As a demonstration of the proposed framework, we apply it to a simulated hybrid system that combines isotropic and patchy particles with octahedral symmetry. In conclusion, not only does the methodology allow one to identify individual crystalline domains but also it detects coherent clusters of a peculiar compact amorphous structure that is not space-filling and lacks any long-range order.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗