Accurate,non-oscillatory,remeshing schemes for particle methods

In this article we propose and validate new remeshing schemes for the simulation of transport equations by particle methods. Particle remeshing is a common way to control the regularity of the particle distribution which is necessary to guarantee the accuracy of particle methods in presence of strong strain in a flow. Using a grid-based analysis, we derive remeshing schemes that can be used in a consistent way at every time-step in a particle method. The schemes are obtained by local corrections of classical third order and fifth order interpolation kernels. The time-step to be used in the resulting push-and-remesh particle method is determined on the basis of rigorous bounds and can significantly exceed values obtained by CFL conditions in usual grid-based Eulerian methods. In addition, we extend the analysis of [5] to obtain TVD remeshing schemes that avoid oscillations of remeshing formulas near sharp variations of the solution. These methods are illustrated in several flow conditions in 1D, 2D and 3D.     

Failure Mechanisms of Plasterboard in Nail Pull Test Determined by X-ray Microtomography and Digital Volume Correlation

To design lightweight plasterboard and optimize the compromise between thermal resistance and mechanical strength, it is important to characterize its strength as assessed with the normative “Nail pull” test. Understanding the phenomenology of this test is the key to identifying the limiting factor in terms of load carrying capacity. In this work, the degradation mechanisms of lightweight plasterboard are analyzed via tests conducted in situ in a laboratory tomograph. Through the analysis of the kinematics by digital volume correlation, the different mechanisms at play up to failure mechanism have been identified, i.e., quasi-elastic regime, failure of the roller coating layer, core compaction and core failure. The compaction of the core by the collapse of porosity in compression is recognized as the limiting factor in terms of compressive strength and tearing resistance.     

Selective and Cooperative Ligand Binding to Antiparallel Human Telomeric DNA G‐Quadruplexes

The quest for ligands that specifically bind to particular G‐quadruplex nucleic acid structures is particularly important to conceive molecules with specific effects on gene expression or telomere maintenance, or conceive structure‐specific molecular probes. Using electrospray mass spectrometry in native conditions, we reveal a highly cooperative and selective 2:1 binding of Cu^II‐tolylterpyridine complexes to human telomeric G‐quadruplexes. Circular dichroism and comparisons of affinities for different sequences reveal a marked preference for antiparallel structures with diagonal loops and/or wide‐medium–narrow‐medium groove‐width order. The cooperativity is attributed to conformational changes in the polymorphic telomeric G‐quadruplex sequences, which convert preferably into an antiparallel three‐quartet topology upon binding of two ligands.     

Assessment of a Two-Way Coupling Methodology Between a Flow and a High-Order Nonlinear Acoustic Unstructured Solvers

A two-way coupling on unstructured meshes between a flow and a high-order acoustic solvers for jet noise prediction is considered. The flow simulation aims at generating acoustic sources in the near field while the acoustic simulation solves the full Euler equations, thanks to a discontinuous Galerkin method, in order to take into account nonlinear acoustic propagation effects. This methodology is firstly validated on academic cases involving nonlinear sound propagation, shock waves and convection of aerodynamic perturbations. The results are compared to analytical solutions and direct computations. A good behaviour of the coupling is found regarding the targeted space applications. An application on a launch pad model is then simulated to demonstrate the robustness and reliability of the present approach.     

Solid-phase syntheses of 6-arylpyridazin-3(2H)-ones

The 3-chloropyridazine moiety was immobilized on a Wang resin, using two different methodologies. The first of these involved direct nucleophilic substitution of 3,6-dichloropyridazine with the alcoholate of Wang resin. The experimental conditions were optimized. The second method involved a Mitsunobu reaction between the Wang resin and 6-chloropyridazin-3-ol during which a problem of regioselectivity was observed. The so-obtained chloropyridazine-containing resins were subsequently reacted with various arylboronic acids under Suzuki conditions. Acid cleavage yielded 6-arylpyridazin-3(2H)-ones with high chemical purity.     

Catalytic syntheses of alternating, stereoregular ethylene/cycloolefin copolymers

The alternating stereospecific copolymerization of ethylene with cycloolefins (cyclopentene, cycloheptene, and cyclooctene) has been investigated with a series of constrained geometry titanium catalysts (CGCs). The metallocene IndSiMe₂(^tBuN)TiCl₂ was found to generate highly alternating and stereoregular cycloolefin-co-ethylene polymers while Me₄CpSiMe₂(^tBuN)TiCl₂ produced alternating atactic polymers. In addition, novel Ti-complexes of the general formula benz[6.7]indenylSiMe₂(^tBuN)TiMe₂ were synthesized and fully characterized. The chiral indenyl Ti complexes were found to produce exclusive 1,2-enchainment of the cycloolefin to generate highly stereoregular and alternating copolymers.     

A neutron scattering study of the structure and water partitioning of selectively deuterated copolymer micelles

We present a scattering study of a selectively deuterated micelle-forming diblock copolymer. The copolymer comprises a partially deuterated polystyrene (d,h-PS) block and an imidazolium-functionalized PS (IL) block. In toluene solutions, the copolymers assemble into elongated micelles where the IL block forms the micelle core. Through dynamic light scattering (DLS) measurements, we obtain the overall size of the micelles. In our small-angle neutron scattering (SANS) studies, we use contrast matching to characterize the IL core and the PS shell of the micelles independently. The PS block forming the micelle shell exhibits either a starlike or brushlike conformation depending upon the size of the core to which it is tethered. We find the IL block to be in an extended conformation, driving the formation of slightly elongated and relatively stiff micelle cores. The elongated micelle core cross-sectional radius and length depend linearly on the length of the IL block. We find that the micelles can sequester a few water molecules for each IL repeat unit; the addition of water slightly increases the cross section of the elongated micelles.     

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2

We present the performance of HADDOCK, our information-driven docking software, in the second edition of the D3R Grand Challenge. In this blind experiment, participants were requested to predict the structures and binding affinities of complexes between the Farnesoid X nuclear receptor and 102 different ligands. The models obtained in Stage1 with HADDOCK and ligand-specific protocol show an average ligand RMSD of 5.1 Å from the crystal structure. Only 6/35 targets were within 2.5 Å RMSD from the reference, which prompted us to investigate the limiting factors and revise our protocol for Stage2. The choice of the receptor conformation appeared to have the strongest influence on the results. Our Stage2 models were of higher quality (13 out of 35 were within 2.5 Å), with an average RMSD of 4.1 Å. The docking protocol was applied to all 102 ligands to generate poses for binding affinity prediction. We developed a modified version of our contact-based binding affinity predictor PRODIGY, using the number of interatomic contacts classified by their type and the intermolecular electrostatic energy. This simple structure-based binding affinity predictor shows a Kendall’s Tau correlation of 0.37 in ranking the ligands (7th best out of 77 methods, 5th/25 groups). Those results were obtained from the average prediction over the top10 poses, irrespective of their similarity/correctness, underscoring the robustness of our simple predictor. This results in an enrichment factor of 2.5 compared to a random predictor for ranking ligands within the top 25%, making it a promising approach to identify lead compounds in virtual screening.