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Results for “structural complexity”
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Spatially Adaptive Stochastic Methods for Mesoscopic Fluid-Structure Interactions in Complex Geometries.
Abstract not provided.
Deep Convolutional Neural Networks as a Rapid Screening Tool for Complex Additively Manufactured Structures.
Abstract not provided.
Methods for SAXS-Based Structure Determination of Biomolecular Complexes
Measurements from small-angle X-ray scattering (SAXS) are highly informative to determine the structures of bimolecular complexes in solution. Here, we describe current and recent SAXS-driven developments, with an emphasis on computational modeling. In particular, accurate methods to computing one theoretical scattering profile from a given structure model are discussed, with a key focus on structure factor coarse-graining and hydration contribution. Methods for reconstructing topological structures from an experimental SAXS profile are currently under active development. We report on several modeling tools designed for conformation generation that make use of either atomic-level or coarse-grained representations. Furthermore, since large, flexible biomolecules can adopt multiple well-defined conformations, a traditional single-conformation SAXS analysis is inappropriate, so we also discuss recent methods that utilize the concept of ensemble optimization, weighing in on the SAXS contributions of a heterogeneous mixture of conformations. These tools will ultimately posit the usefulness of SAXS data beyond a simple space-filling approach by providing a reliable structure characterization of biomolecular complexes under physiological conditions.
Assessment of electronic structure methods for the determination of the ground spin states of Fe( ii ), Fe( iii ) and Fe( iv ) complexes
Our ability to understand and simulate the reactions catalyzed by iron depends strongly on our ability to predict the relative energetics of spin states. In this work, we studied the electronic structures of Fe 2+ ion, gaseous FeO and 14 iron complexes using Kohn–Sham density functional theory with particular focus on determining the ground spin state of these species as well as the magnitudes of relevant spin-state energy splittings. The 14 iron complexes investigated in this work have hexacoordinate geometries of which seven are Fe(II), five are Fe(III) and two are Fe(IV) complexes. These are calculated using 20 exchange–correlation functionals. In particular, we use a local spin density approximation (LSDA) – GVWN5, four generalized gradient approximations (GGAs) – BLYP, PBE, OPBE and OLYP, two non-separable gradient approximations (NGAs) – GAM and N12, two meta-GGAs – M06-L and M11-L, a meta-NGA – MN15-L, five hybrid GGAs – B3LYP, B3LYP*, PBE0, B97-3 and SOGGA11-X, four hybrid meta-GGAs – M06, PW6B95, MPW1B95 and M08-SO and a hybrid meta-NGA – MN15. The density functional results are compared to reference data, which include experimental results as well as the results of diffusion Monte Carlo (DMC) calculations and ligand field theory estimates from the literature. For the Fe 2+ ion, all functionals except M11-L correctly predict the ground spin state to be quintet. However, quantitatively, most of the functionals are not close to the experimentally determined spin-state splitting energies. For FeO all functionals predict quintet to be the ground spin state. For the 14 iron complexes, the hybrid functionals B3LYP, MPW1B95 and MN15 correctly predict the ground spin state of 13 out of 14 complexes and PW6B95 gets all the 14 complexes right. Here, the local functionals, OPBE, OLYP and M06-L, predict the correct ground spin state for 12 out of 14 complexes. Two of the tested functionals are not recommended to be used for this type of study, in particular M08-SO and M11-L, because M08-SO systematically overstabilizes the high spin state, and M11-L systematically overstabilizes the low spin state.
Manipulation of Lignin Monomer Composition Combined with the Introduction of Monolignol Conjugate Biosynthesis Leads to Synergistic Changes in Lignin Structure
Abstract The complexity of lignin structure impedes efficient cell wall digestibility. Native lignin is composed of a mixture of three dominant monomers, coupled together through a variety of linkages. Work over the past few decades has demonstrated that lignin composition can be altered through a variety of mutational and transgenic approaches such that the polymer is derived almost entirely from a single monomer. In this study, we investigated changes to lignin structure and digestibility in Arabidopsis thaliana in near-single-monolignol transgenics and mutants and determined whether novel monolignol conjugates, produced by a FERULOYL-CoA MONOLIGNOL TRANSFERASE (FMT) or a p-COUMAROYL-CoA MONOLIGNOL TRANSFERASE (PMT), could be integrated into these novel polymers to further improve saccharification efficiency. Monolignol conjugates, including a new conjugate of interest, p-coumaryl p-coumarate, were successfully integrated into high-H, high-G and high-S lignins in A. thaliana. Regardless of lignin composition, FMT- and PMT-expressing plants produced monolignol ferulates and monolignol p-coumarates, respectively, and incorporated them into their lignin. Through the production and incorporation of monolignol conjugates into near-single-monolignol lignins, we demonstrated that substrate availability, rather than monolignol transferase substrate preference, is the most important determining factor in the production of monolignol conjugates, and lignin composition helps dictate cell wall digestibility.
Engineered unique elastic modes at a BaTiO 3 /2x1-Ge(001) interface
Here, the strong interaction at an interface between a substrate and thin film leads to epitaxy and provides a means of inducing structural changes in the epitaxial film. These induced material phases often exhibit technologically relevant electronic, magnetic, and functional properties. The 2×1 surface of a Ge(001) substrate applies a unique type of epitaxial constraint on thin films of the perovskite oxide BaTiO 3 where a change in bonding and symmetry at the interface leads to a non-bulk-like crystal structure of the BaTiO 3 . While the complex crystal structure is predicted using first-principles theory, it is further shown that the details of the structure are a consequence of hidden phases found in the bulk elastic response of the BaTiO 3 induced by the symmetry of forces exerted by the germanium substrate.
Development of Methodologies for the Estimation of Thermal Properties Associated with Aerospace Vehicles
A thermal stress analysis is an important aspect in the design of aerospace structures and vehicles such as the High Speed Civil Transport (HSCT) at the National Aeronautics and Space Administration Langley Research Center (NASA-LaRC). These structures are complex and are often composed of numerous components fabricated from a variety of different materials. The thermal loads on these structures induce temperature variations within the structure, which in turn result in the development of thermal stresses. Therefore, a thermal stress analysis requires knowledge of the temperature distributions within the structures which consequently necessitates the need for accurate knowledge of the thermal properties, boundary conditions and thermal interface conditions associated with the structural materials. The goal of this proposed multi-year research effort was to develop estimation methodologies for the determination of the thermal properties and interface conditions associated with aerospace vehicles. Specific objectives focused on the development and implementation of optimal experimental design strategies and methodologies for the estimation of thermal properties associated with simple composite and honeycomb structures. The strategy used in this multi-year research effort was to first develop methodologies for relatively simple systems and then systematically modify these methodologies to analyze complex structures. This can be thought of as a building block approach. This strategy was intended to promote maximum usability of the resulting estimation procedure by NASA-LARC researchers through the design of in-house experimentation procedures and through the use of an existing general purpose finite element software.
Crystal structure of EGFR T790M/C797S/V948R in complex with EAI045
Lung cancer is the leading cause of cancer deaths. Epidermal growth factor receptor (EGFR) kinase domain mutations are a common cause of non-small cell lung cancers (NSCLCs), a major subtype of lung cancers. Patients harboring most of these mutations respond well to the anti-EGFR tyrosine kinase inhibitors (TKIs) gefitinib and erlotinib initially, but soon develop resistance to them in about half of the cases due to the emergence of the gatekeeper mutation T790M. The third-generation TKIs such as AZD9291, HM61713, CO-1686 and WZ4002 can overcome T790M through covalent binding to the EGFR kinase through Cys 797, but ultimately lose their efficacy upon emergence of the C797S mutation that abolishes the covalent bonding. Therefore to develop new TKIs to overcome EGFR drug-resistant mutants harboring T790M/C797S is urgently demanded. EAI001 and EAI045 are a new type of EGFR TKIs that bind to EGFR reversibly and not relying on Cys 797. EAI045 in combination with cetuximab is effective in mouse models of lung cancer driven by EGFR L858R/T790M and L858R/T790M/C797S. Here we report the crystal structure of EGFR T790M/C797S/V948R in complex with EAI045, and compare it to EGFR T790M/V948R in complex with EAI001. The complex structure reveals why EAI045 binds tighter to EGFR than does EAI001, and why EAI001 and EAI045 prefer binding to EGFR T790M. The knowledge may facilitate future drug development studies targeting this very important cancer target.
Single-Site Carbon-Supported Metal-Oxo Complexes in Heterogeneous Catalysis: Structure, Reactivity, and Mechanism
When early transition metal complexes are molecularly grafted onto catalyst supports, well-defined, surface-bound species are created, which are highly active and selective single-site heterogeneous catalysts (SSHCs) for diverse chemical transformations. Further, in this minireview, we analyze and summarize a less conventional type of SSHC in which molybdenum dioxo species are grafted onto unusual carbon-unsaturated scaffolds, such as activated carbon, reduced graphene oxide, and carbon nanohorns. The choice of earth-abundant, low-toxicity, versatile metal constituents, and various carbon supports illustrates “catalyst by design” principles and yields insights into new catalytic systems of both academic and technological interest. Here, we summarize experimental and computational investigations of the bonding, electronic structure, reaction scope, and mechanistic pathways of these unusual catalysts.
Modular fabrication and characterization of complex silicon carbide composite structures Advanced Reactor Technologies (ART) Research Final Report (Feb 2015 – May 2017)
Advanced ceramic materials exhibit properties that enable safety and fuel cycle efficiency improvements in advanced nuclear reactors. In order to fully exploit these desirable properties, new processing techniques are required to produce the complex geometries inherent to nuclear fuel assemblies and support structures. Through this project, the state of complex SiC-SiC composite fabrication for nuclear components has advanced significantly. New methods to produce complex SiC-SiC composite structures have been demonstrated in the form factors needed for in-core structural components in advanced high temperature nuclear reactors. Advanced characterization techniques have been employed to demonstrate that these complex SiC-SiC composite structures provide the strength, toughness and hermeticity required for service in harsh reactor conditions. The complex structures produced in this project represent a significant step forward in leveraging the excellent high temperature strength, resistance to neutron induced damage, and low neutron cross section of silicon carbide in nuclear applications.
Improved wax mold technique forms complex passages in solid structures
Low-cost fabricating technique produces minute, complex air passages in fluidic devices. Air jet interactions in these function as electronic and electromechanical control systems. Wax cores are fabricated without distortion by two-wax process using nonsoluble pattern-wax and water-soluble wax. Significant steps in fabrication process are discussed.
Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation
Abstract Mutations in RAS and PI3Kα are major drivers of human cancer. Their interaction plays a crucial role in activating PI3Kα and amplifying the PI3K-AKT-mTOR pathway. Disrupting RAS-PI3Kα interaction enhances survival in lung and skin cancer models and reduces tumor growth and angiogenesis, although the structural details of this interaction remain unclear. Here, we present structures of KRAS, RRAS2, and MRAS bound to the catalytic subunit (p110α) of PI3Kα, elucidating the interaction interfaces and local conformational changes upon complex formation. Structural and mutational analyses highlighted key residues in RAS and PI3Kα impacting binding affinity and revealed isoform-specific differences at the interaction interface in RAS and PI3K isoforms, providing a rationale for their differential affinities. Notably, in the RAS-p110α complex structures, RAS interaction with p110α is limited to the RAS-binding domain and does not involve the kinase domain. This study underscores the pivotal role of the RAS-PI3Kα interaction in PI3Kα activation and provides a blueprint for designing PI3Kα isoform-specific inhibitors to disrupt this interaction.
The formation and structure of mechano-synthesized nanocrystalline Sr{sub 3}Fe{sub 2}O{sub 6.4}: XRD Rietveld, Mössabuer and XPS analyses
Highlights: • The formation of mechano-synthesized nanocrystalline Sr{sub 3}Fe{sub 2}O{sub 7−δ} is investigated. • Pre-milling the reactants substantially lowers the formation temperature. • The core and surface structures were studied. • XRD and {sup 57}Fe Mössbauer spectroscopic analyses indicate the δ-value to be 0.60. • XPS shows a complex surface structure for the mechanosynthesized Sr{sub 3}Fe{sub 2}O{sub 7−δ} nanoparticles. - Abstract: The influence of ball milling and subsequent sintering of a 3:1 molar mixture of SrCO{sub 3} and α-Fe{sub 2}O{sub 3} on the formation of Sr{sub 3}Fe{sub 2}O{sub 7−δ} double perovskite is investigated with different analytical techniques. Milling the mixture for 110 h leads to the formation of SrCO{sub 3}-α-Fe{sub 2}O{sub 3} nanocomposites and the structural deformation of α-Fe{sub 2}O{sub 3} via the incorporation of Sr{sup 2+} ions. Subsequent sintering of the pre-milled reactants’ mixture has led to the partial formation of an SrFeO{sub 3} perovskite-related phase in the temperature range 400–600 °C. This was followed by the progressive development of an Sr{sub 3}Fe{sub 2}O{sub 7−δ} phase that continued to increase with increasing sintering temperature until a single-phased nanocrystalline Sr{sub 3}Fe{sub 2}O{sub 7−δ} phase was attained at 950 °C (12 h). This temperature is ∼350 °C lower than the temperature at which the material is prepared conventionally using the ceramic method. The evolution of different structural phases during the reaction process is discussed. Rietveld refinement of the X-ray diffraction data shows a value of 0.60 for the oxygen deficiency δ, in consistency with the Fe{sup 3+}/Fe{sup 4+} ratio derived from the {sup 57}Fe Mössbauer data recorded at both 300 K and 78 K. The Mössbauer data suggests that the Sr{sub 3}Fe{sub 2}O{sub 6.4} nanoparticles are superparamagnetic with blocking temperatures below 78 K. The surfaces of the Sr{sub 3}Fe{sub 2}O{sub 6.4} nanoparticles were shown to have a complex structure and composition relative to those of their cores with traces of SrCO{sub 3}, SrO and SrFeO{sub 3−δ} being detected.
Preliminary criteria for the fracture control of space shuttle structures
The complex and multidisciplinary factors are presented which relate to the prevention of structural failure due to the initiation or propagation of cracks or crack-like defects. The fracture control criteria are applicable to space shuttle components which are: (1) susceptible to cracking or fracture on the basis of anticipated loads and environment, and (2) critical to either crew safety or system performance. The criteria define the design, fabrication, environmental control, inspection, maintenance, repair, and verification procedures required for adequate fracture control.
ODIN: Characterizing the Three-dimensional Structure of Two Protocluster Complexes at z = 3.1
We present a detailed study of the 3D morphology of two extended associations of multiple protoclusters at z = 3.1. These protocluster "complexes," designated COSMOS-z3.1-A and COSMOS-z3.1-C, are the most prominent overdensities of z = 3.1 Lyα emitters (LAEs) identified in the COSMOS field by the One-hundred-deg$^{2}$ DECam Imaging in Narrowbands survey. These protocluster complexes have been followed up with extensive spectroscopy from Keck, Gemini, and DESI. Using a probabilistic method that combines photometrically selected and spectroscopically confirmed LAEs, we reconstruct the 3D structure of these complexes on scales of ≈50 cMpc. We validate our reconstruction method using the IllustrisTNG300-1 cosmological hydrodynamical simulation and show that it consistently outperforms approaches relying solely on spectroscopic data. The resulting 3D maps reveal that both complexes are irregular and elongated along a single axis, emphasizing the impact of sightline on our perception of structure morphology. The complexes consist of multiple density peaks, 10 in COSMOS-z3.1-A and 4 in COSMOS-z3.1-C. The former is confirmed to be a proto-supercluster, similar to Hyperion at z = 2.4 but observed at an even earlier epoch. Multiple "tails" connected to the cores of the density peaks are seen, likely representing cosmic filaments feeding into these extremely overdense regions. The 3D reconstructions further provide strong evidence that Lyα blobs preferentially reside in the outskirts of the highest density regions. Descendant mass estimates of the density peaks suggest that COSMOS-z3.1-A and COSMOS-z3.1-C will evolve to become ultramassive structures by z = 0, with total masses log ( M / M ,⊙ ,) ≳ 15.3 , exceeding that of Coma.