On how structural model variability influence transonic aeroelasticity stability.

This paper considers the ways in which structural model parameter variability can in?uence aeroelastic stability. Previous work on formulating the stability calculation (with the Euler equations providing the aerodynamic predictions) is exploited to use Monte Carlo, Interval and Perturbation calculations to allow this question to be investigated. Three routes are identi?ed. The ?rst involves variable normal mode frequencies only. The second involves normal mode frequencies and mode shapes. Finally, the third, in addition to normal mode frequencies and mode shapes, also includes their in?uence on the static equilibrium. Previous work has suggested only considering route 1, which allows signi?cant gains in computational e?ciency if reduced order models can be built for the aerodynamics. However, results in the current paper show that neglecting route 2 can give misleading results for the ?utter onset prediction.

How Structural Model Variability Influences Transonic Aeroelastic Stability

This paper considers the ways in which structural model parameter variability can influence aeroelastic stability. Previous work on formulating the stability calculation (with the Euler equations providing the aerodynamic predictions) is exploited to use Monte Carlo, interval, and perturbation calculations to allow this question to be investigated. Three routes are identified. The first involves variable normal-mode frequencies only. The second involves normal-mode frequencies and shapes. Finally, the third, in addition to normal-mode frequencies and shapes, also includes their influence on the static equilibrium. Previous work has suggested only considering the first route, which allows significant gains in computational efficiency if reduced-order models can be built for the aerodynamics. However, results in the current paper show that neglecting the mode-shape variation can give misleading results for the flutter-onset prediction, complicating the development of reduced aerodynamic models for variability analysis.

Atomistic Insights into Rhodopsin Activation from a Dynamic Model

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.

Transonic Aeroelastic Stability Predictions Under the Influence of Structural Variability

Flutter prediction as currently practiced is almost always deterministic in nature, based on a single structural model that is assumed to represent a fleet of aircraft. However, it is also recognized that there can be significant structural variability, even for different flights of the same aircraft. The safety factor used for flutter clearance is in part meant to account for this variability. Simulation tools can, however, represent the consequences of structural variability in the flutter predictions, providing extra information that could be useful in planning physical tests and assessing risk. The main problem arising for this type of calculation when using high-fidelity tools based on computational fluid dynamics is the computational cost. The current paper uses an eigenvalue-based stability method together with Euler-level aerodynamics and different methods for propagating structural variability to stability predictions. The propagation methods are Monte Carlo, perturbation, and interval analysis. The feasibility of this type of analysis is demonstrated. Results are presented for the Goland wing and a generic fighter configuration.

Model reduction for nonlinear aeroelasticity using the Discrete Empirical Interpolation Method

A novel surrogate model is proposed in lieu of computational fluid dynamic (CFD) code for fast nonlinear aerodynamic modeling. First, a nonlinear function is identified on selected interpolation points defined by discrete empirical interpolation method (DEIM). The flow field is then reconstructed by a least square approximation of flow modes extracted by proper orthogonal decomposition (POD). The proposed model is applied in the prediction of limit cycle oscillation for a plunge/pitch airfoil and a delta wing with linear structural model, results are validate against a time accurate CFD-FEM code. The results show the model is able to replicate the aerodynamic forces and flow fields with sufficient accuracy while requiring a fraction of CFD cost.

Reducing Uncertainty in Aeroelastic Flutter Boundaries Using Experimental Data

Flutter prediction as currently practiced is usually deterministic, with a single structural model used to represent an aircraft. By using interval analysis to take into account structural variability, recent work has demonstrated that small changes in the structure can lead to very large changes in the altitude at which
utter occurs (Marques, Badcock, et al., J. Aircraft, 2010). In this follow-up work we examine the same phenomenon using probabilistic collocation (PC), an uncertainty quantification technique which can eficiently propagate multivariate stochastic input through a simulation code,
in this case an eigenvalue-based fluid-structure stability code. The resulting analysis predicts the consequences of an uncertain structure on incidence of
utter in probabilistic terms { information that could be useful in planning
flight-tests and assessing the risk of structural failure. The uncertainty in
utter altitude is confirmed to be substantial. Assuming that the structural uncertainty represents a epistemic uncertainty regarding the
structure, it may be reduced with the availability of additional information { for example aeroelastic response data from a flight-test. Such data is used to update the structural uncertainty using Bayes' theorem. The consequent
utter uncertainty is significantly reduced across the entire Mach number range.

Modeled structure of a G-protein-coupled receptor:The cholecystokinin-1 receptor

The Cholecystokinin-1 receptor (CCK1R) mediates actions of CCK in areas of the central nervous system and of the gut. It is a potential target to treat a number of diseases. As for all G-protein-coupled receptors, docking of ligands into modeled CCK1R binding site should greatly help to understand intrinsic mechanisms of activation. Here, we describe the procedure we used to progressively build a structural model for the CCK1R, to integrated, and on the basis of site-directed mutagenesis data on its binding site. Reliability of the CCK1R model was confirmed by interaction networks that involved conserved and functionally crucial motifs in G-protein-coupled receptors, such as Glu/Asp-Arg-Tyr and Asn-Pro-Xaa-Xaa-Tyr motifs. In addition, the 3-D structure of CCK1R-bound CCK resembled that determined by NMR in a lipid environment. The derived computational model was also used for revealing binding modes of several nonpeptide ligands and for rationalizing ligand structure-activity relationships known from experiments. Our findings indeed support that our "validated CCK1R model" could be used to study the intrinsic mechanism of CCK1R activation and design new ligands.

Structure of molten 1,3-dimethylimidazolium chloride using neutron diffraction

The model room temperature ionic liquid, 1,3-dimethylimidazolium chloride, has been studied by neutron diffraction for the first time. The diffraction data are used to derive a structural model of this liquid using Empirical Potential Structure Refinement. The model obtained indicates that significant charge ordering is present in the liquid salt and that the local order in this liquid closely resembles that found in the solid state. As in the crystal structure, hydrogen-bonding interactions between the ring hydrogens and the chloride dominate the structure. The model is compared with the data reported previously for both simple alkyl substituted imidazolium halides and binary mixtures with AlCl3. (C) 2003 American Institute of Physics.

The optimized geometric structure of the (0001) surface of α-Fe 2O3

A tridimensional model of α-Fe₂O₃ and models of (0001) and (1102) surfaces on it were built. Then the structural optimization of the (0001) surface was presented which explored the influence of the system scale and the terminal surface configuration. Four different models including two different system scale structures (MODEL□ and MODEL□) and two different terminal structures (MODEL□ and MODEL□) were analyzed in this paper. It was concluded that the boundary effect was more important in a smaller system in the structure optimization. And the Fe-terminated was more stable than the O-terminated structure which was agreed with the experiences, this structural model can be used in further work including the monatomic adsorption/desorption and the chemical reactions on this surface.

Structure and Catalytic Activity of Gold in Low-Temperature CO Oxidation

Structures and catalytic activities of Au thin films supported at anatase TiO(2)(101)) and a Au substrate are studied by using density functional theory calculations. The results show that O(2) can hardly adsorb at flat and stepped Au thin films, even supported by fully reduced TiO(2)(101) that can highly disperse Au atoms and offer strong electronic promotion. Interestingly, in both oxide-supported and pure Au. systems, wire-structured Au can adsorb both CO and O(2) rather strongly, and kinetic analysis suggests its high catalytic activity for low-temperature CO oxidation. The d-band center of Au at the catalytic site is determined to account for the unusual activity of the wire-structured film. A generalized structural model based on the wire-structured film is proposed for active Au, and possible support effects are discussed: Selected oxide surfaces can disperse Au atoms and stabilize the formation of a filmlike structure; they may also serve as a template for the preferential arrangement of Au atoms in a wire structure under low Au coverage.

ArnT proteins that catalyse the glycosylation of lipopolysaccharide share common features with bacterial N-oligosaccharyltransferases

ArnT is a glycosyltransferase that catalyses the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) to the lipid A moiety of the lipopolysaccharide. This is a critical modification enabling bacteria to resist killing by antimicrobial peptides. ArnT is an integral inner membrane protein consisting of 13 predicted transmembrane helices and a large periplasmic C-terminal domain. We report here the identification of a functional motif with a canonical consensus sequence DEXRYAX(5)MX(3)GXWX(9)YFEKPX(4)W spanning the first periplasmic loop, which is highly conserved in all ArnT proteins examined. Site-directed mutagenesis demonstrated the contribution of this motif in ArnT function, suggesting that these proteins have a common mechanism. We also demonstrate that the Burkholderia cenocepacia and Salmonella enterica serovar Typhimurium ArnT C-terminal domain is required for polymyxin B resistance in vivo. Deletion of the C-terminal domain in B. cenocepacia ArnT resulted in a protein with significantly reduced in vitro binding to a lipid A fluorescent substrate and unable to catalyse lipid A modification with L-Ara4N. An in silico predicted structural model of ArnT strongly resembled the tertiary structure of Campylobacter lari PglB, a bacterial oligosaccharyltransferase involved in protein N-glycosylation. Therefore, distantly related oligosaccharyltransferases from ArnT and PglB families operating on lipid and polypeptide substrates, respectively, share unexpected structural similarity that could not be predicted from direct amino acid sequence comparisons. We propose that lipid A and protein glycosylation enzymes share a conserved catalytic mechanism despite their evolutionary divergence.

Relative energetics and structural properties of zirconia using a self-consistent tight-binding model

We describe an empirical, self-consistent, orthogonal tight-binding model for zirconia, which allows for the polarizability of the anions at dipole and quadrupole levels and for crystal field splitting of the cation d orbitals, This is achieved by mixing the orbitals of different symmetry on a site with coupling coefficients driven by the Coulomb potentials up to octapole level. The additional forces on atoms due to the self-consistency and polarizabilities are exactly obtained by straightforward electrostatics, by analogy with the Hellmann-Feynman theorem as applied in first-principles calculations. The model correctly orders the zero temperature energies of all zirconia polymorphs. The Zr-O matrix elements of the Hamiltonian, which measure covalency, make a greater contribution than the polarizability to the energy differences between phases. Results for elastic constants of the cubic and tetragonal phases and phonon frequencies of the cubic phase are also presented and compared with some experimental data and first-principles calculations. We suggest that the model will be useful for studying finite temperature effects by means of molecular dynamics.