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Fluid-Thermal-Structural Interactions in Ramp-Induced Shock-Wave Boundary-Layer Interactions at Mach 6
Shock-wave boundary-layer interactions (SWBLI) pose unique challenges for the slender airframes and sharp control surfaces characteristic of high-speed airbreathing aircraft. Spikes in pressure and thermal loading have been shown to occur in SWBLI regions; thus, predicting their location and behavior proves critical for assuring aircraft structural integrity and fatigue resilience. SWBLIs frequently lead to severe turbulent boundary-layer separation and corresponding unsteady motions characterized by a wide range of frequencies. Low-frequency motion has been shown to couple with the structure of a compliant panel, and turbulent boundary layers thus present a particular danger for thin control surfaces. Previous studies have shown that the thermal loading on a compliant panel in a ramp-induced SWBLI may have a signi cant impact on the panel vibrations. A multitude of studies has investigated the heating on rigid structures, but a charactrization of the heating effects on compliant structures is necessary to fully understand the fluid-thermal-structural interactions (FTSI) occurring in ramp-induced SWBLIs. This studuses infrared thermography and high-frequency Kulite pressure transducers to examine the heating loads on rigid and compliant ramps at various angles and flow conditions at Mach 6.
Synthesis and Characterization of the First 2 D Neptunyl Structure Stabilized by Side-on Cation-Cation Interactions
Cation–cation interaction: A new 2 D sheet structure containing a side-on cation–cation interaction (CCI) has been synthesized and characterized (see figure). Unprecedentedly, no chelating ligands between the cations are present. We explore the nature of the side-on interaction and ligand effects by using a variety of quantum chemical methods. The spin–orbit-coupled ground state mixes singlet, triplet, and quintet-pure spin states.
BECN2 interacts with ATG14 through a metastable coiled-coil to mediate autophagy: BECN2 CCD Structure and Interaction with ATG14
ATG14 binding to BECN/Beclin homologs is essential for autophagy, a critical catabolic homeostasis pathway. Here, we show that the α-helical, coiled-coil domain (CCD) of BECN2, a recently identified mammalian BECN1 paralog, forms an antiparallel, curved homodimer with seven pairs of nonideal packing interactions, while the BECN2 CCD and ATG14 CCD form a parallel, curved heterodimer stabilized by multiple, conserved polar interactions. Compared to BECN1, the BECN2 CCD forms a weaker homodimer, but binds more tightly to the ATG14 CCD. Mutation of nonideal BECN2 interface residues to more ideal pairs improves homodimer self-association and thermal stability. Unlike BECN1, all BECN2 CCD mutants bind ATG14, although more weakly than wild type. Thus, polar BECN2 CCD interface residues result in a metastable homodimer, facilitating dissociation, but enable better interactions with polar ATG14 residues stabilizing the BECN2:ATG14 heterodimer. These structure-based mechanistic differences in BECN1 and BECN2 homodimerization and heterodimerization likely dictate competitive ATG14 recruitment.
Structure and interactions of the C-terminal metal binding domain of Archaeoglobus fulgidus CopA
Abstract not provided
Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP 2 -containing membranes: Modeling of DAT N-Terminus/PIP 2 Interactions
The dopamine transporter (DAT) is a transmembrane protein belonging to the family of neurotransmitter:sodium symporters (NSS). Members of the NSS are responsible for the clearance of neurotransmitters from the synaptic cleft, and for their translocation back into the presynaptic nerve terminal. The DAT contains long intracellular N- and C-terminal domains that are strongly implicated in the transporter function. The N-terminus (N-term), in particular, regulates the reverse transport (efflux) of the substrate through DAT. Currently, the molecular mechanisms of the efflux remain elusive in large part due to lack of structural information on the N-terminal segment. Here we report a computational model of the N-term of the human DAT (hDAT), obtained through an ab initio structure prediction, in combination with extensive atomistic molecular dynamics (MD) simulations in the context of a lipid membrane. Our analysis reveals that whereas the N-term is a highly dynamic domain, it contains secondary structure elements that remain stable in the long MD trajectories of interactions with the bilayer (totaling >2.2 μs). Combining MD simulations with continuum mean-field modeling we found that the N-term engages with lipid membranes through electrostatic interactions with the charged lipids PIP 2 (phosphatidylinositol 4,5-Biphosphate) or PS (phosphatidylserine) that are present in these bilayers. We identify specific motifs along the N-term implicated in such interactions and show that differential modes of N-term/membrane association result in differential positioning of the structured segments on the membrane surface. These results will inform future structure-based studies that will elucidate the mechanistic role of the N-term in DAT function.
Interaction of Pure Alumina Refractory with FeO–SiO 2 and FeO–SiO 2 –CaO Slags Relevant to the Novel Flash Ironmaking Technology
Not provided.
Fluctuating Hydrodynamic Methods for Fluid-Structure Interactions in Confined Channel Geometries
Computational methods are developed for the study of fluid-structure interactions subject to thermal fluctuations when conned within channels having slit-like geometry. The methods take into account the hydrodynamic coupling and diusivity of microstructures when influenced by their proximity to no-slip walls. We develop stochastic numerical methods subject to no-slip boundary conditions using a staggered nite volume discretization. We show that by imposing an exact fluctuation-dissipation condition to discretize the stochastic driving elds combined with using an exact projection method to enforce incompressibility is sucient to ensure results consistent with statistical mechanics. We demonstrate our methods by investigating how the proximity of ellipsoidal colloids to the channel wall eects their active hydrodynamic responses and passive diusivity. We also study the collective dynamics of a large number of particles by considering the intermediate scattering functions for the relaxation of density fluctuations. We expect our introduced stochastic computational methods to be applicable broadly to applications in which confinement effects play an important role in the dynamics of microstructures subject to hydrodynamic coupling and thermal fluctuations. uctuations.
Interaction of Iron with Alumina Refractory Under Flash Ironmaking Conditions
A novel flash ironmaking technology (FIT) based on the direct reduction of iron ore concentrate by a reducing gas such as hydrogen, natural gas, or coal gas has been developed at the University of Utah. A proper choice of refractories is expected to play an important role in the development of FIT and its scale-up. In this work, the interaction of iron with alumina refractory under flash ironmaking conditions has been investigated. A thermodynamic basis for the interaction phenomena has been developed by considering the Fe-Al-O system, and a kinetic model based on solid-state diffusion is proposed to describe the growth of the hercynite (FeAl{sub 2}O{sub 4}) spinel formed as a result of the interaction between Fe, O (from H{sub 2}O and CO{sub 2}), and Al{sub 2}O{sub 3}. Experiments were conducted with Fe powders and pure Al{sub 2}O{sub 3} in the temperature range 1200 to 1500 °C under gas atmospheres relevant to flash ironmaking, and the reacted samples were analyzed using XRD, SEM-EDX, and EPMA techniques. The analyses of reacted samples confirmed the formation of the hercynite (FeAl{sub 2}O{sub 4}) spinel phase and the thickness of the FeAl{sub 2}O{sub 4} spinel as measured using elemental line scans in SEM-EDX and EPMA varied in the range of 0.5 to 1.3 mm. Results showed that the proposed model suitably describes the growth of the hercynite spinel layer, which obeyed the parabolic rate law at all temperatures. The parabolic rate constants were obtained and the diffusion-controlled growth of the FeAl{sub 2}O{sub 4} layer strongly depended on temperature. Furthermore, using the kinetic model, an expression for the effective diffusivity ( (D{sub eff})-bar ) was obtained and its values at the experimental temperatures were determined. The solid-state diffusion was an activated process, as expected, with an activation energy value of 231 kJ/mol.
The role of correlation and solvation in ion interactions with B-DNA
Ionic atmosphere around nucleic acids plays important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle X-ray scattering (ASAXS) can provide important insights into the structure and energetics of the ionic atmosphere but are time- and resource-intensive. In this paper, we demonstrate the use of classical density functional theory to model DNA-ion interactions and explore the balance between ion-DNA, ion-water, and ion-ion interactions. In particular, we compute the distribution of RbCl, SrCl2, and CoHexCl3 (cobalt hexammine chlo- ride) around a B-form DNA molecule. The accuracy of the DFT calculations was assessed by comparison between simulated and experimental ASAXS curves. As expected, these calculations revealed significant differences between the monovalent, divalent, and trivalent cations. About half of the DNA-bound Rb+ ions penetrate into the minor groove of the DNA and half adsorb on the DNA strands. The fraction of cations in the minor groove decreases for the larger Sr2+ ions and becomes zero for CoHex3+ ions, which all adsorb on the DNA strands. The distribution of CoHex3+ ions is mainly determined by Coulomb interactions, while ion-correlation forces play a central role in the monovalent Rb+ distribution and a combination of ion-correlation and hydration forces affect the Sr2+ distribution around DNA.
Ab initio study of interstitial cluster interaction with Re, Os, and Ta in W
Not Available
Tunable twin stability and an accurate magnesium interatomic potential for dislocation-twin interactions
Not Available
Complexity of Blocking Bivalent Protein–Protein Interactions: Development of a Highly Potent Inhibitor of the Menin–Mixed-Lineage Leukemia Interaction
The protein–protein interaction between menin and mixed-lineage leukemia 1 (MLL1) plays an important role in development of acute leukemia with translocations of the MLL1 gene and in solid tumors. Here, we report the development of a new generation of menin–MLL1 inhibitors identified by structure-based optimization of the thienopyrimidine class of compounds. This work resulted in compound 28 (MI-1481), which showed very potent inhibition of the menin–MLL1 interaction (IC 50 = 3.6 nM), representing the most potent reversible menin–MLL1 inhibitor reported to date. The crystal structure of the menin-28 complex revealed a hydrogen bond with Glu366 and hydrophobic interactions, which contributed to strong inhibitory activity of 28. Compound 28 also demonstrates pronounced activity in MLL leukemia cells and in vivo in MLL leukemia models. Thus, we report 28 is a valuable menin–MLL1 inhibitor that can be used for potential therapeutic applications and in further studies regarding the role of menin in cancer.
Tailoring Interfacial Interactions via Polymer-Grafted Nanoparticles Improves Performance of Parts Created by 3D Printing
Abstract not provided
Interfacial Reactivity and Speciation Emerging from Na-Montmorillonite Interactions with Water and Formic Acid at 200 °C: Insights from Reactive Molecular Dynamics Simulations, Infrared Spectroscopy, and X-ray Scattering Measurements
Reactive organic fluid - mineral interactions at elevated temperatures contribute to the evolution of planetary matter. One of the less studied but important transformations in this regard involves the reactions of formic acid with naturally occurring clays such as sodium montmorillonite. To advance a mechanistic understanding of these interactions, we use ReaxFF reactive molecular dynamics simulations in conjunction with infrared (IR) spectroscopy and X-ray scattering experiments to investigate the speciation behavior of water-formic acid mixtures on sodium montmorillonite interfaces at 473 K and 1 atm. Using a newly developed reactive forcefield, we show that the experimental IR spectra of unreacted and reacted mixture can be accurately reproduced by ReaxFF/MD. We further benchmark the simulation predictions of sodium carbonate and bicarbonate formation in the clay interlayers using Small and Wide-Angle X-ray Scattering measurements. Subsequently, leveraging the benchmarked forcefield, we interrogate the pathway of speciation reactions with emphasis on carbonate, formate, and hydroxide groups elucidating the energetics, transition states, intermediates, and preferred products. Further, we also delineate the differences in reactivities and catalytic effects of clay edges, facets, and interlayers owing to their local chemical environments, which have far reaching consequences in their speciation behavior. The experimental and simulation approaches described in this study and the transferable forcefields can be applied translationally to advance the science of clay-fluid interactions for several applications including subsurface fluid storage and recovery and clay-pollutant dynamics.
A series of Ln-p-chlorobenzoic acid–terpyridine complexes: lanthanide contraction effects, supramolecular interactions and luminescent behavior
Fifteen new lanthanide p-chlorobenzoic acid complexes, [PrL3(terpy)(H2O)]2 (1), [LnL3(terpy)(H2O)]2 (Ln = Nd (2), Sm (3), and Eu (4)), and [LnL3(terpy)(H2O)] (Ln = Sm (3'), Eu (4'), Gd (5), Tb (6), Dy (7), Ho (8), Er (9), Tm (10), Yb (11), Lu (12), and Y (13); HL: p-chlorobenzoic acid; terpy: 2,2':6',2''-terpyridine), have been synthesized hydrothermally at varying temperatures and structurally characterized by single crystal and powder X-ray diffraction. The series is comprised of binuclear molecular units (Pr–Eu) that give way to mononuclear molecular complexes (Sm–Y) as the lanthanide contraction takes effect. All fifteen complexes feature a tridentate terpyridine ligand, p-chlorobenzoic acid ligands exhibiting multiple binding modes, bidentate, bridging bidentate, and monodentate, and a bound water molecule. Binuclear complexes 1–4 are stitched together via intermolecular interactions: aromatic–aromatic interactions for 1, halogen•••halogen interactions for 2–4, to form 1D chains. Mononuclear complexes 3', 4', and 5–13 utilize supramolecular hydrogen and halogen bonding to form 2D sheets. Visible and near-IR solid state luminescence studies were performed on complexes 2, 3, 3', 4, 4', 6, 7 and 11 and the characteristic visible luminescence of Sm(III), Eu(III), Tb(III), and Dy(III) was exhibited. The near-IR spectra of the Nd(III) and Yb(III) complexes exhibit weak characteristic luminescence, showing that terpy can act as a sensitizing chromophore in these systems.
Universal scaling of potential energy functions describing intermolecular interactions. II. The halide-water and alkali metal-water interactions
The scaled versions of the newly introduced [S. S. Xantheas and J. C. Werhahn, J. Chem. Phys.141, 064117 (2014)] generalized forms of some popular potential energy functions (PEFs) describing intermolecular interactions – Mie, Lennard-Jones, Morse, and Buckingham exponential-6 – have been used to fit the ab initio relaxed approach paths and fixed approach paths for the halide-water, X - (H 2 O), X = F, Cl, Br, I, and alkali metal-water, M + (H 2 O), M = Li, Na, K, Rb, Cs, interactions. The generalized forms of those PEFs have an additional parameter with respect to the original forms and produce fits to the ab initio data that are between one and two orders of magnitude better in the χ 2 than the original PEFs. They were found to describe both the long-range, minimum and repulsive wall of the respective potential energy surfaces quite accurately. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gBe-6) potentials were found to best fit the ab initio data for these two classes of ion-water interactions. Finally, the fitted values of the parameter of the (eM) and (gBe-6) PEFs that control the repulsive wall of the potential correlate remarkably well with the ionic radii of the halide and alkali metal ions.