Computing clique and chromatic number of circular-perfect graphs in polynomial time

A main result of combinatorial optimization is that clique and chromatic number of a perfect graph are computable in polynomial time (Grötschel et al. in Combinatorica 1(2):169–197, 1981). Perfect graphs have the key property that clique and chromatic number coincide for all induced subgraphs; we address the question whether the algorithmic results for perfect graphs can be extended to graph classes where the chromatic number of all members is bounded by the clique number plus one. We consider a well-studied superclass of perfect graphs satisfying this property, the circular-perfect graphs, and show that for such graphs both clique and chromatic number are computable in polynomial time as well. In addition, we discuss the polynomial time computability of further graph parameters for certain subclasses of circular-perfect graphs. All the results strongly rely upon Lovász’s Theta function.     

Dimension Reduction for Finite Trees in \varvec{\ell _1}

We show that every $n$ -point tree metric admits a $(1+\varepsilon )$ -embedding into $\ell _1^{C(\varepsilon ) \log n}$ , for every $\varepsilon > 0$ , where $C(\varepsilon ) \le O\big ((\frac{1}{\varepsilon })^4 \log \frac{1}{\varepsilon })\big )$ . This matches the natural volume lower bound up to a factor depending only on $\varepsilon $ . Previously, it was unknown whether even complete binary trees on $n$ nodes could be embedded in $\ell _1^{O(\log n)}$ with $O(1)$ distortion. For complete $d$ -ary trees, our construction achieves $C(\varepsilon ) \le O\big (\frac{1}{\varepsilon ^2}\big )$ .     

An Adaptive Interacting Wang–Landau Algorithm for Automatic Density Exploration

While statisticians are well-accustomed to performing exploratory analysis in the modeling stage of an analysis, the notion of conducting preliminary general-purpose exploratory analysis in the Monte Carlo stage (or more generally, the model-fitting stage) of an analysis is an area that we feel deserves much further attention. Toward this aim, this article proposes a general-purpose algorithm for automatic density exploration. The proposed exploration algorithm combines and expands upon components from various adaptive Markov chain Monte Carlo methods, with the Wang–Landau algorithm at its heart. Additionally, the algorithm is run on interacting parallel chains—a feature that both decreases computational cost as well as stabilizes the algorithm, improving its ability to explore the density. Performance of this new parallel adaptive Wang–Landau algorithm is studied in several applications. Through a Bayesian variable selection example, we demonstrate the convergence gains obtained with interacting chains. The ability of the algorithm’s adaptive proposal to induce mode-jumping is illustrated through a Bayesian mixture modeling application. Last, through a two-dimensional Ising model, the authors demonstrate the ability of the algorithm to overcome the high correlations encountered in spatial models. Supplemental materials are available online.     

Stimulated Raman X waves in ultrashort optical pulse filamentation

We demonstrate that ultrashort pulse filamentation in liquids with strong Raman gain leads to the spontaneous formation of nonlinear X waves at a Raman-shifted wavelength. We measured as much as 75% energy conversion efficiency into a Raman X wave in ethanol starting from 1 ps pulses due to the group velocity matching between the pump and Raman X pulses. Large Raman gain of a weak seed signal was observed in water, associated with a strong spatiotemporal transformation of the seed into an X wave.     

Polarization-sensitive full-field optical coherence tomography

We present a polarization-sensitive full-field optical coherence tomography system that can produce high-resolution images of the linear retardance and reflectivity properties of biological media. En face images can be delivered at a frame rate of 3.5 Hz by combination of interferometric images acquired by two CCD cameras in an interference microscope illuminated with a tungsten halogen lamp. Isotropic spatial resolution of approximately 1.0 microm is achieved. The technique is demonstrated on ex vivo muscle tissues.     

Accuracy evaluation of an optical lattice clock with bosonic atoms

We report what we believe to be the first accuracy evaluation of an optical lattice clock based on the S01-->P03 transition of an alkaline earth boson, namely, Sr88 atoms. This transition has been enabled by using a static coupling magnetic field. The clock frequency is determined to be 429228066418009(32)Hz. The isotopic shift between Sr87 and Sr88 is 62188135Hz with fractional uncertainty 5x10(-7). We discuss the necessary conditions to reach a clock accuracy of 10(-17) or less by using this scheme.     

Membrane protein selectively oriented on solid support and reconstituted into a lipid membrane

Mimetic functional membranes on solid support are now emerging for the development of membrane biosensor or for the study of membrane-mediated processes and should have an important impact on biodiagnostics. We established a method to reconstitute a membrane protein into a lipid membrane in a selective orientation on a solid support. Membrane protein OprM, a component of OprM-MexA-MexB multidrug efflux pump, solubilized in detergent was immobilized via its extracellular domain on aminosilane-modified silica surface. The oriented protein was reconstituted into a lipid membrane by detergent removal. The membrane protein reconstitution process carried out on silica nanoparticles and on planar silica surfaces was followed by cryo-electron microscopy (cryo-EM) and quartz crystal microbalance with dissipation monitoring (QCM-D) respectively. The selective protein orientation on aminosilane-modified silica surface was assessed by cryo-EM and was compared to the nonspecific protein deposition on silica surface. Finally, the binding of MexA, a periplasmic component of the tripartite efflux complex, was monitored with QCM-D on the oriented OprM protein monolayer. The large adsorbed mass gave a direct evidence of the high affinity of MexA with the periplasmic helical part of OprM.     

Salting-out effect induced by temperature cycling on a water/nonionic surfactant/oil system

This paper presents original effects induced by temperature cycling on the transitional phase inversion of emulsions, stabilized by a nonionic polyethoxylated C18E6 surfactant model. The phase inversion follow-up is performed by electrical conductivity measurements, which involves focusing the study on the shape and location of the emulsion inversion region. In that way, new observations are brought out as a gradual evolution of the emulsion inversion along the cycling process. Two alternative approaches are considered for tackling these results: (i) first, a molecular approach regarding the particular organization and rearrangement of water clusters surrounding the surfactant polymer polar head, and (ii) second, a thermodynamic approach only considering the whole Gibbs free energy of the system. The volumic approaches are transposed, here, to the water/oil interface, and disclose that the phase inversion zone is included in a metastable region, able to stabilize for a given temperature, either metastable O/W emulsions or stable W/O ones. In that way, this study proposes novel and complementary insights into the phenomena governing the emulsion phase inversion.     

Mechanistic aspects of the solid-state transformation of ammonium cyanate to urea at high pressure

The chemical transformation of ammonium cyanate into urea has been of interest to many generations of scientists since its discovery by Friedrich W?hler in 1828. Although widely studied both experimentally and theoretically, several mechanistic aspects of this reaction remain to be understood. In this paper, we apply computational methods to investigate the behavior of ammonium cyanate in the solid state under high pressure, employing a theoretical approach based on the self-consistent-charges density-functional tight-binding method (SCC-DFTB). The ammonium cyanate crystal structure was relaxed under external pressure ranging from 0 to 700 GPa, leading to the identification of five structural phases. Significantly, the phase at highest pressure (above 535 GPa) corresponds to the formation of urea molecules. At ca. 25 GPa, there is a phase transition of ammonium cyanate (from tetragonal P4/nmm to monoclinic P21/m) involving a rearrangement of the ammonium cyanate molecules. This transformation is critical for the subsequent transformation to urea. The crystalline phase of urea obtained above 535 GPa also has P21/m symmetry (Z = 2). This polymorph of urea has never been reported previously. Comparisons to the known (tetragonal) polymorph of urea found experimentally at ambient pressure suggests that the new polymorph is more stable above ca. 8 GPa. Our computational studies show that the transformation of ammonium cyanate into urea is strongly exothermic (enthalpy change -170 kJ mol-1 per formula unit between 530 and 535 GPa). The proposed mechanism for this transformation involves the transfer of two hydrogen atoms of the ammonium cation toward nitrogen atoms of neighboring cyanate anions, and the remaining NH2 group creates a C-NH2 bond with the cyanate unit.     

Chiral discrimination in host-guest supramolecular complexes. Understanding enantioselectivity and solid solution behaviors by using spectroscopic methods and chemical sensors

Diastereomeric host-guest associations formed between permethylated-beta-cyclodextrin (TMbeta-Cd) and the two enantiomers of p-bromophenylethanol (pBrPE) were characterized in aqueous solution by NMR spectroscopy, revealing similar inclusion geometries and weak binding constants, whatever the guest configuration. These features were confirmed by hydrogenation experiments, and do not allow to account for the ability of TMbeta-Cd to resolve racemic pBrPE by successive crystallizations [Grandeury, A.; Petit, S.; Gouhier, G.; Agasse, V.; Coquerel, G. Tetrahedron: Asymmetry 2003, 14, 2143-2152]. The analysis, by means of solid-state NMR, oxidation experiments, and solubility measurements, of the two crystalline phases containing known proportions of guest enantiomers revealed identical inclusion geometries in a given phase, irrespective of the enantiomeric composition. The corresponding solid solutions were further characterized by the determination of an isothermal section (40 degrees C) in the relevant ternary phase diagram. It appears from all these data that chiral resolution mechanisms in this system can only be envisaged in terms of nucleation conditions of each crystal form (with its specific inclusion geometry) and enantiomeric recognition at crystal solution interfaces during the growth of each crystal packing.