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Results for “core crystallization”

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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family of enzymes, which catalyzes the removal of both 3'- and 5'-DNA phosphodiester adducts. Importantly, it is capable of reducing the anticancer effects of type I topoisomerase (TOP1) inhibitors by repairing the stalled covalent complexes of TOP1 with DNA. It achieves this by promoting the hydrolysis of the phosphodiester bond between the Y723 residue of human TOP1 and the 3'-phosphate of its DNA substrate. Blocking TDP1 function is an attractive means of enhancing the efficacy of TOP1 inhibitors and overcoming drug resistance. Previously, we reported the use of an X-ray crystallographic screen of more than 600 fragments to identify small molecule variations on phthalic acid and hydroxyquinoline motifs that bind within the TDP1 catalytic pocket. Yet, the majority of these compounds showed limited (millimolar) TDP1 inhibitory potencies. We now report examining a 21 000-member library of drug-like Small Molecules in Microarray (SMM) format for their ability to bind Alexa Fluor 647 (AF647)-labeled TDP1. The screen identified structurally similar N,2-diphenylimidazo[1,2-a]pyrazin-3-amines as TDP1 binders and catalytic inhibitors. We then explored the core heterocycle skeleton using one-pot Groebke–Blackburn–Bienayme multicomponent reactions and arrived at analogs having higher inhibitory potencies. Solving TDP1 co-crystal structures of a subset of compounds showed their binding at the TDP1 catalytic site, while mimicking substrate interactions. Although our original fragment screen differed significantly from the current microarray protocol, both methods identified ligand–protein interactions containing highly similar elements. Importantly inhibitors identified through the SMM approach show competitive inhibition against TDP1 and access the catalytic phosphate-binding pocket, while simultaneously providing extensions into both the substrate DNA and peptide-binding channels. As such, they represent a platform for further elaboration of trivalent ligands, that could serve as a new genre of potent TDP1 inhibitors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Kinematics and dynamics of disclination lines in three-dimensional nematics

An exact kinematic law for the motion of disclination lines in nematic liquid crystals as a function of the tensor order parameter Q is derived. Unlike other order parameter fields that become singular at their respective defect cores, the tensor order parameter remains regular. Following earlier experimental and theoretical work, the disclination core is defined to be the line where the uniaxial and biaxial order parameters are equal, or equivalently, where the two largest eigenvalues of Q cross. This allows an exact expression relating the velocity of the line to spatial and temporal derivatives of Q on the line, to be specified by a dynamical model for the evolution of the nematic. By introducing a linear core approximation for Q, analytical results are given for several prototypical configurations, including line interactions and motion, loop annihilation, and the response to external fields and shear flows. Behaviour that follows from topological constraints or defect geometry is highlighted. Finally, the analytic results are shown to be in agreement with three-dimensional numerical calculations based on a singular Maier–Saupe free energy that allows for anisotropic elasticity.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Uncertainty Quantification Framework for Predicting Material Response with Large Number of Parameters: Application to Creep Prediction in Ferritic-Martensitic Steels Using Combined Crystal Plasticity and Grain Boundary Models

This paper presents an uncertainty quantification (UQ) framework for the physics-based model prediction of material response with a large number of parameters. The application problem presented in this work is that of predicting creep in Grade 91 steel at 600°C. The material response is defined with a physically based microstructural model with constitutive equations emulating several observed phenomena in Grade 91 and embodied into an explicit geometry mesoscale finite element model for prior austenite grains and grain boundaries. Creep within the grains and in grain boundaries are represented by crystal plasticity for dislocation motion and a physics-based model for cavity growth and nucleation, respectively. The creep behavior of this material is influenced by several parameters, some of which have a wide range of variation based on experimental data. UQ combined with microstructural modeling can discover the core microstructural causes of experimental variability, leading to improved materials with lower variability in critical long-term material properties. In this study, we investigate the model's uncertainty to identify material properties that may be modified during production to increase creep life and analyze different components of the crystal plasticity model for improvements. For this purpose, a quantity of interest is defined as time to minimum creep rate, which correlates well to the creep failure of the material. A deep neural network model was trained and validated to be used as a surrogate for the finite element model. Then, a variance-based sensitivity analysis is performed on the surrogate model to find the Sobol indices of the input parameters in respect to the output quantity of interest. The Sobol indices are used to reduce the dimensionality of the model. Generalized polynomial chaos expansion is used on the reduced basis models to propagate the uncertainty from the input parameters to the quantity of interest using the deep neural network surrogate model. These results are benchmarked against uncertainty propagation using Monte Carlo simulations. In conclusion, the UQ performed through the reduced basis model captures almost all the uncertainty in the model with significantly fewer simulations, making it possible to perform the UQ directly via simulations with the finite element model rather than surrogate machine-learned models.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Electrically Pumped Epitaxially Regrown GaSb-Based Type-I Quantum-Well Surface-Emitting Lasers with Buried High-Index-Contrast Photonic Crystal Layer

Epitaxially regrown electrically pumped photonic crystal surface-emitting lasers (PCSELs) emitting near 2 and 2.6 μm are designed, fabricated, and characterized. A high-index-contrast photonic crystal layer is incorporated into the GaSb-based laser heterostructure by air-hole-retaining epitaxial regrowth. A square lattice of triangular holes is etched in the top waveguide core layer of the incomplete laser heterostructure. The nanopatterned surface is subsequently cleaned and regrown with AlGaAsSb p-cladding material. Transmission electron microscopy studies demonstrate uniform regrowth over the nanopatterned GaSb surface. The selected regrowth regimes yield a buried 2D array of elongated air-holes. The diode PCSELs based on moderately etched nanopatterns demonstrate band-edge lasing near 2 μm up to room temperatures. The cascade diode PCSELs operate near 2.6 μm with minimum threshold current densities of about 500 A cm -2 achieved at 180 K. The devices generate mW level output in narrow divergence beam emitted from the window in substrate contact. The angle-resolved electroluminescence measurements reveal a four-sub-band band structure with an apparent photonic bandgap corresponding to the buried high-index-contrast square photonic crystal layer. Finally, the PCSELs made of heterostructures supporting two modes in the vertical direction demonstrate two sets of sub-bands showing anti-crossing-like interaction.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

The yeast ALA synthase C‐terminus positively controls enzyme structure and function

Abstract 5‐Aminolevulinic acid synthase (ALAS) is a pyridoxal 5′‐phosphate (PLP)‐dependent enzyme that catalyzes the first and rate‐limiting step of heme biosynthesis in α‐proteobacteria and several non‐plant eukaryotes. All ALAS homologs contain a highly conserved catalytic core, but eukaryotes also have a unique C‐terminal extension that plays a role in enzyme regulation. Several mutations in this region are implicated in multiple blood disorders in humans. In Saccharomyces cerevisiae ALAS (Hem1), the C‐terminal extension wraps around the homodimer core to contact conserved ALAS motifs proximal to the opposite active site. To determine the importance of these Hem1 C‐terminal interactions, we determined the crystal structure of S. cerevisiae Hem1 lacking the terminal 14 amino acids (Hem1 ΔCT). With truncation of the C‐terminal extension, we show structurally and biochemically that multiple catalytic motifs become flexible, including an antiparallel β‐sheet important to Fold‐Type I PLP‐dependent enzymes. The changes in protein conformation result in an altered cofactor microenvironment, decreased enzyme activity and catalytic efficiency, and ablation of subunit cooperativity. These findings suggest that the eukaryotic ALAS C‐terminus has a homolog‐specific role in mediating heme biosynthesis, indicating a mechanism for autoregulation that can be exploited to allosterically modulate heme biosynthesis in different organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein

The molecular basis for the severity and rapid spread of the COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04-Å resolution by X-ray crystallography. The structure reveals a ~60-residue core similar to SARS-CoV-2 ORF7a, with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. A covalent disulfide-linked dimer is formed through an N-terminal sequence specific to SARS-CoV-2, while a separate noncovalent interface is formed by another SARS-CoV-2-specific sequence, 73 YIDI 76 . Together, the presence of these interfaces shows how SARS-CoV-2 ORF8 can form unique large-scale assemblies not possible for SARS-CoV, potentially mediating unique immune suppression and evasion activities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A parallel and performance portable implementation of a full-field crystal plasticity model

We have developed a parallel implementation of an Elasto-Viscoplastic Fast Fourier Transform-based (EVPFFT) micromechanical solver to enable computationally efficient crystal plasticity modeling for polycrystalline materials. Our primary focus lies in achieving performance portability, allowing a single EVPFFT implementation to run optimally on various homogeneous architectures, including multi-core Central Processing Units (CPUs), as well as on heterogeneous computer architectures comprising multi-core CPUs and Graphics Processing Units (GPUs) from different vendors. To accomplish this goal, we have leveraged MATAR, a C++ software library that simplifies the creation and utilization of multidimensional dense or sparse matrix and array data structures. These data structures are designed to be portable across diverse architectures through the use of Kokkos, a performance-portable library. Additionally, we have employed the Message Passing Interface (MPI) to efficiently distribute the computational workload among processors. The heFFTe (Highly Efficient FFT for Exascale) library is used to facilitate the performance portability of the fast Fourier transforms (FFTs) computation. The computational performance of EVPFFT is evaluated and presented in terms of parallel scalability and simulation runtime on different high-performance computing (HPC) architectures. As a result, the utility of the developed framework to efficiently simulate the micro-mechanical fields in polycrystalline microstructures in engineering applications is discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structure and antigenicity of the divergent human astrovirus VA1 capsid spike

Human astrovirus (HAstV) is a known cause of viral gastroenteritis in children worldwide, but HAstV can cause also severe and systemic infections in immunocompromised patients. There are three clades of HAstV: classical, MLB, and VA/HMO. While all three clades are found in gastrointestinal samples, HAstV-VA/HMO is the main clade associated with meningitis and encephalitis in immunocompromised patients. To understand how the HAstV-VA/HMO can infect the central nervous system, we investigated its sequence-divergent capsid spike, which functions in cell attachment and may influence viral tropism. Here we report the high-resolution crystal structures of the HAstV-VA1 capsid spike from strains isolated from patients with gastrointestinal and neuronal disease. The HAstV-VA1 spike forms a dimer and shares a core beta-barrel structure with other astrovirus capsid spikes but is otherwise strikingly different, suggesting that HAstV-VA1 may utilize a different cell receptor, and an infection competition assay supports this hypothesis. Furthermore, by mapping the capsid protease cleavage site onto the structure, the maturation and assembly of the HAstV-VA1 capsid is revealed. Finally, comparison of gastrointestinal and neuronal HAstV-VA1 sequences, structures, and antigenicity suggests that neuronal HAstV-VA1 strains may have acquired immune escape mutations. Overall, our studies on the HAstV-VA1 capsid spike lay a foundation to further investigate the biology of HAstV-VA/HMO and to develop vaccines and therapeutics targeting it.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Effects of Hydrogen on the Phase Relations in Fe-FeS at Pressures of Mars-Sized Bodies

The large radius, and therefore low density, of the Martian core found in the InSight mission data analysis highlights the importance of considering other light elements besides sulfur (S), which has been considered as the main light element for Mars for decades. Hydrogen (H) is abundant in the solar system and becomes siderophile at high pressures. Although Fe-S and Fe-H systems have been studied individually, the Fe-S-H ternary system has only been investigated up to 16 GPa and 1723 K. We have investigated the Fe-S-H system at pressures and temperatures (P-T) relevant to the cores of Mars-sized planets (up to 45 GPa and well above the melting temperature of FeS) in the laser-heated diamond anvil cell combined with in situ synchrotron X-ray diffraction. Here we found that sufficient hydrogen leads to the disappearance of Fe 3 S at high P-T. Instead, separate Fe-H and Fe-S phases appear at 23–35 GPa. At pressures above 35 GPa, we found a new phase appearing while Fe-S phases disappear and Fe-H phases remain. Our analysis indicates that the new phase likely contains both S and H in the crystal structure (tentatively FeS x H y where x ≈ 1 and y ≈ 1). The observed pressure-dependent changes in the phase relation may be important for understanding the structure and dynamics of the Martian core and the cores of Mars-sized exoplanets.

58 GEOSCIENCES↗
DOE OSTI2025

The [M 6 (S 2 C 2 Ph 2 ) 6 ] (M = Ni, Pd, Pt) Series: Multielectron Reservoirs That Sustain Ligand-Based Oxidations and Metal-Based Reductions

A complete [M 6 (S 2 C 2 R 2 ) 6 ] series (M = Ni (1), Pd (2), Pt (3); R = Ph), the rarest variety among homoleptic dithiolene transition-metal compounds, has been prepared by reaction between [M(S 2 C 2 Ph 2 ) 2 ] and a M 0 source. The platinum member of this set is the first of its type. Diffraction-quality crystals, grown with high reproducibility by evaporation from PhNO 2 solutions, reveal fully reduced [Ph 2 C 2 S 2 ] 2– dianions and an octahedral M 6 core that is reduced to C 2 symmetry by the fusion of a mononuclear D 2h [M(S 2 C 2 Ph 2 ) 2 ] fragment upon a C 4 -symmetric base. The [Ni 6 (S 2 C 2 Ph 2 ) 2 ] 1– monoanion, prepared by Cp* 2 Co reduction, shows only modest structural differences from its neutral counterpart. In CH 2 Cl 2 , 1 and 2 can undergo two reductions and an oxidation, while 3 sustains two reductions and two oxidations. In benzonitrile, 1 sustains three reversible oxidations at potentials that are shifted appreciably to less positive values. The cathodic processes are shown by density functional theory (DFT) calculations to involve an MO largely of metal–sulfur composition that has contributions throughout the C 4 -symmetric pentametallic base of the assembly, while the oxidations are largely ligand-based and confined to the monometallic [M(S 2 C 2 Ph 2 ) 2 ] cap. The absorption spectra are marked by multiple overlapping bands that produce a continuous, tapering absorption profile of unresolved shoulders and swells.

Ligands↗
DOE OSTI2025

Crystalline Peptoid Nanofibers with a Single-Unit Cell Cross Section

Ultranarrow crystalline one-dimensional nanostructures formed from soft materials facilitate precise structural control in nanomaterial design, which is essential for biomedicine and nanotechnology applications. Systematic control of their hierarchical structure is challenging due to the complexities of simultaneously manipulating multiple noncovalent interactions at such small scales. We employed a polypeptoid crystal motif as a supramolecular synthon to engineer ultranarrow crystalline nanofibers constrained to a single lattice axis by incorporating a single ionizable side chain into the hydrophobic core of a nanosheet-forming peptoid. Cryogenic transmission electron microscopy of the nanofibers revealed detailed molecular arrangements of a unit-cell cross-section and the presence of distinct pH-dependent lattice isoforms that resulted in morphological transformations. Molecular dynamics simulations demonstrated that the ionizable side chain plays a critical role in changing the local conformation of the unit cell, which further impacts the dimensionality of hierarchical structures. Moreover, these fibers were readily functionalized with biological ligands to afford one-dimensional (1D) protein arrays. This approach for the high-precision bottom-up assembly of ultranarrow 1D nanostructures offers significant potential for developing novel biomimetic nanostructures.

Lee, Yen Jea↗
DOE OSTI2025

Significant Efficiency Enhancements in Non‐Y Series Acceptors by the Addition of Outer Side Chains

Abstract Most current highly efficient organic solar cells utilize small molecules like Y6 and its derivatives as electron acceptors in the photoactive layer. In this work, a small molecule acceptor, SC8‐IT4F, is developed through outer side chain engineering on the terminal thiophene of a conjugated 6,12‐dihydro‐dithienoindeno[2,3‐d:2′,3′‐d′]‐s‐indaceno[1,2‐b:5,6‐b′]dithiophene (IDTT) central core. Compared to the reference molecule C8‐IT4F, which lacks outer side chains, SC8‐IT4F displays notable differences in molecule geometry (as shown by simulations), thermal behavior, single‐crystal packing, and film morphology. Blend films of SC8‐IT4F and the polymer donor PM6 exhibit larger carrier mobilities, longer carrier lifetimes, and reduced recombination compared to C8‐IT4F, resulting in improved device performance. Binary photovoltaic devices based on the PM6:SC8‐IT4F films reveal an optimal efficiency over 15%, which is one of the best values for non‐Y type small molecule acceptors (SMAs). The resultant devices also show better thermal and operational stability than the control PM6:L8‐BO devices. SC8‐IT4F and its blend exhibit a higher relative degree of crystallinity and π coherence length, compared to C8‐IT4F samples, beneficial for charge transport and device performance. The results indicate that outer side chain engineering on existing small electron acceptors can be a promising molecular design strategy for further pursuing high‐performance organic solar cells.

He, Qiao [Department of Chemistry and Centre for P↗
DOE OSTI2024

Exascale Dislocation Simulator

ExaDiS, or Exascale Dislocation Simulator, is a set of software modules written to enable numerical simulations of large groups of moving and interacting dislocations, line defects in crystals responsible for crystal plasticity. By tracking time evolution of sufficiently large dislocation ensembles, ExaDiS predicts plasticity response and plastic strength of crystalline materials. ExaDiS is built around a library of core functions for Discrete Dislocation Dynamics method specifically written to perform efficient computations on GPUs.

Bertin, Nicolas↗
DOE OSTI2023

Structure and Magnetic Properties of Homoleptic Trivalent Tris(alkyl)lanthanides

Six new solvent-free, homoleptic paramagnetic tris(alkyl)lanthanides Ln{C(SiHMe 2 ) 3 } 3 (1Ln) and Ln{C(SiHMe 2 ) 2 Ph} 3 (2Ln) (Ln = Gd, Dy, and Er) were synthesized to investigate the magnetic properties of 4f organometallic compounds stabilized by secondary Ln←H–Si and benzylic interactions. The unit cell of 1Gd contains one independent molecule (Z = 2), while 1Dy and 1Er crystallize with four independent isostructural molecules per unit cell (Z = 16). In all molecules, as in other 1Ln compounds, the three tris(dimethylsilyl)methyl ligands form a trigonal planar LnC 3 core, and six secondary interactions involving Ln←H–Si bonding in Ln{C(SiHMe 2 ) 3 } 3 form above and below the equatorial plane. Two and five crystallographically independent molecules of each 2Ln (2Gd, Z = 8; 2Dy, Z = 20) form with three π-coordinated phenyl groups in addition to either one or two secondary Ln←H–Si interactions per molecule. The packing of these midseries organolanthanide compounds contrasts the single crystallographically unique molecules in previously reported La{C(SiHMe 2 ) 3 } 3 (1La, Z = 2, Z' = 1) and La{C(SiHMe 2 ) 2 Ph} 3 (2La, Z = 2, Z' = 1/3). 2La doped with 2Dy can adopt the crystallographic structure of 2La, which promotes magnetic properties, namely a higher χ m T value at low temperatures as well as stronger magnetic anisotropy. The ac susceptibility data for 10% 2Dy doped into 2La suggests slow relaxation at low temperatures with a relaxation barrier of ~45 K. The computed saturated magnetization of 1Er (M ≈ 4.5 μ B ) and 1Dy (M ≈ 6 μ B ) matches the experimental values, while the computed value for 2Dy better matches the value measured for 2Dy diluted in 2La (M ≈ 5 μ B ). Gas-phase calculations predict that the ground-state and first excited-state multiplet separations are larger for 1Er than 2Er, while the ordering for dysprosium is 1Dy > 2Dy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Verifying the structure-property-performance relationship of Y6-based small molecule acceptors by alkoxy-side chain isomerization and conjugated skeleton asymmetry

Non-fullerene small molecule acceptors (NF-SMAs) such as Y6 derivatives were the current working horse for the top performing polymer solar cells (PSCs). For this reason, numerous chemical modifications have been explored for establishing structure–property-performance relationship for Y6-based NF-SMAs. In this work, we explored the isomerization on asymmetrical Y6 derivatives by varying the position of alkoxy side chain on the thiophene linkage between the core and one of the end groups of Y6. The isomers with differences in conformational restriction raised by noncovalent interactions as well as steric hindrance revealed distinctive behavior in crystallization and polymorphism, which led to a significant contrast in PSC performances. Here the X-TO1 molecule with alkoxy side chain facing the end group (outward) displayed preferred molecular configuration and polymorph, delivering power conversion efficiency (PCE) of 15.63%, while its isomer X-TO2 showed coexisted polymorphs significantly increased the charge recombination in the PSC devices led to a low PCE around 3%. This structure–property-performance relationship not only highlighted the elegancy of isomerization in tuning the photovoltaic performances but also identified polymorphism as one of the causes for impairing photovoltaic performances of PSCs.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Constraining Flexibility in the MIL-88 Topology through Integration of 3-Dimensional Linkers

Metal–organic frameworks (MOFs) are a class of crystalline, nanoporous materials that are recognized for their tunability. While some MOFs demonstrate flexibility, this characteristic can pose challenges in achieving precise pore control or establishing permanent porosity. Specifically, MIL-88B, is notable for its high flexibility, as it is constructed from metal trimer clusters and 2-dimensional linkers (2DLs) featuring planar, aromatic cores, allowing significant structural changes. In this study, we synthesized two new MOFs, NU-2010 and NU-2011, which are structurally analogous to MIL-88B but incorporate ditopic 3-dimensional linkers (3DLs) with sterically bulky cores and higher symmetry. Our aim was to investigate whether the introduction of 3DLs could mitigate the flexibility observed in MIL-88B. We employed a combination of single crystal and powder X-ray diffraction techniques to assess the flexibility of MIL-88B, NU-2010, and NU-2011 under various conditions including thermal activation, solvent exchange, and temperature changes. Furthermore, our findings indicate that incorporating 3DLs significantly reduces framework flexibility in NU-2010 and NU-2011 relative to MIL-88B.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗