Self-organizing core-shell nanostructures: spontaneous accumulation of dye in the core of doped silica nanoparticles

The process of formation of silica nanoparticles doped with a newly synthesized pyrene derivative has been investigated by means of fluorescence steady-state and time-resolved spectroscopy. The changes in the photophysical properties of the fluorophore were correlated to the increase of the nanoparticles hydrodynamic volume measured via dynamic light scattering (DLS) allowing us to determine the radial profile of the concentration of the dye. Experiments performed at a "low" degree of doping show that the fluorophore is almost completely included considerably before the end of the nanoparticles growth, allowing us to identify a self-organizing core-shell substructure. A strong enhancement of the fluorescence of the dye and a corresponding increase of its excited-state lifetime was observed upon its inclusion as a result of the shielding effect from molecular oxygen due to the silica matrix, a situation confirmed by the absence of the oxygen singlet emission in the near-infrared luminescence spectra. In the case of "high" loading, on the other hand, a heavily doped core showing an excimeric-like emission is first formed. Further growth leads to the formation of layers where the concentration of dye gradually decreases and the monomeric emission becomes relevant. The effect of the degree of doping on the kinetics of growth is also reported. At both concentration regimes, ultrafiltration experiments revealed the complete inclusion of the dye molecules. The average number of dye molecule per nanoparticles was also determined.     

The vibrational spectra of the cyanide ligand revisited. Bridging cyanides

The nu(CN) vibrational spectra of cyanide groups bridging two metal atoms present a confused picture. Factors relevant to the interpretation of the available data are reviewed. Some mechanisms for frequency change, relative to the corresponding terminal species, are made more quantitative than previously described, and others are highlighted for the first time. The kinematic effect is much less important than previously assumed. It seems that an effect responsible for the major part of the frequency increase upon bridging commonly observed is the cation electric field, together with concomitant relaxation (the IVSE model). However, a contribution may well come from the change in the sigma bonding in the CN unit.     

Dynamics of cell membrane passive depolarization: a phase portrait

Does a persistent blockage of the ionic pumps bring cell membrane voltage to zero? This apparently trivial question of basic cellular Biology stirred up an intriguing problem of nonlinear dynamics. A 3-ion model based on continuity and charge conservation proves that membrane voltage actually sets on a negative value, meaning that chemical equilibrium is never reached, rather an inversion of the Na+ concentration gradient occurs, usually hours after the blockage of the pumps. Experimental tests carried out with PC12 cells incubated with Oubaine for a period of 24 hours show an increase of cytosolic Na+ of about 266 mM/l with respect to a control sample. The result is compatible with an inversion of the Na+ gradient, which eventually brings the membrane voltage to a negative value. Reactivation of the Na+-K+ pumps even after a prolonged period of blockage (late repolarization) should lead to repolarization and revival of the cell. In the 3D space of the ionic concentrations, the dynamics of passive depolarization reveals an intriguing topology, all trajectories being stacked in parallel planes, each set ending to a unique fixed point via an infinitely dense set of lines. The dynamics of repolarization has a different phase portrait, especially in the case of late repolarization. Thus, a sequence of depolarization- repolarization cycles may result in a path wandering in the phase space, or in a closed loop, depending on the timing of the sequence.     

Zinc phthalocyanines-mediated photodynamic therapy induces cell death in adenocarcinoma cells

A panel of eight Zn-phthalocyanines (Zn-Pcs) (1)-(8), differently substituted on the benzo units, was synthesized either by direct cyclic-tetramerization of substituted phthalonitriles (compounds 1 and 2), or leading from the easily available tetrasulphonyl phthalocyanine to yield the sulfonamido derivatives 3 and 4, or else via the chloromethylation of precedent Zn-Pc followed by reaction with nucleophiles affording the dicationic Zn-Pcs (5) and (6) or the neutral Zn-Pcs (7) and (8). The phototoxicity of these new compounds was evaluated in vitro on human colon adenocarcinoma cell line (HCT116), and their effect compared with those induced by porfimer sodium. The results are reported as IC₅₀ values, following exposure of the cells to different Zn-Pcs concentration and irradiation with a 500 W tungsten/halogen white lamp. The cationic Zn-Pc (5) and (6) together with the Zn-Pc (7), featuring 12 methoxy groups, were found good or fairly good photosensitizers while the more lipophilic Zn-Pcs (1)-(4) and (8) were found devoid of activity.     

Inference and Learning in a Latent Variable Model for Beta Distributed Interval Data

Latent Variable Models (LVMs) are well established tools to accomplish a range of different data processing tasks. Applications exploit the ability of LVMs to identify latent data structure in order to improve data (e.g., through denoising) or to estimate the relation between latent causes and measurements in medical data. In the latter case, LVMs in the form of noisy-OR Bayes nets represent the standard approach to relate binary latents (which represent diseases) to binary observables (which represent symptoms). Bayes nets with binary representation for symptoms may be perceived as a coarse approximation, however. In practice, real disease symptoms can range from absent over mild and intermediate to very severe. Therefore, using diseases/symptoms relations as motivation, we here ask how standard noisy-OR Bayes nets can be generalized to incorporate continuous observables, e.g., variables that model symptom severity in an interval from healthy to pathological. This transition from binary to interval data poses a number of challenges including a transition from a Bernoulli to a Beta distribution to model symptom statistics. While noisy-OR-like approaches are constrained to model how causes determine the observables’ mean values, the use of Beta distributions additionally provides (and also requires) that the causes determine the observables’ variances. To meet the challenges emerging when generalizing from Bernoulli to Beta distributed observables, we investigate a novel LVM that uses a maximum non-linearity to model how the latents determine means and variances of the observables. Given the model and the goal of likelihood maximization, we then leverage recent theoretical results to derive an Expectation Maximization (EM) algorithm for the suggested LVM. We further show how variational EM can be used to efficiently scale the approach to large networks. Experimental results finally illustrate the efficacy of the proposed model using both synthetic and real data sets. Importantly, we show that the model produces reliable results in estimating causes using proofs of concepts and first tests based on real medical data and on images.     

Asymptotic Resonance, Interaction of Modes and Subharmonic Bifurcation

We study the existence of small amplitude oscillations near elliptic equilibria of autonomous systems, which mix different normal modes. The reference problem is the Fermi-Pasta-Ulam β-model: a chain of nonlinear oscillators with nearest-neighborhood interaction. We develop a new bifurcation approach that locates secondary bifurcations from the unimodal primary branches. Two sufficient conditions for bifurcation are given: one involves only the arithmetic properties of the eigenvalues of the linearized system (asymptotic resonance), while the other takes into account the nonlinear character of the interaction between normal modes (nonlinear coupling). Both conditions are checked for the Fermi-Pasta-Ulam problem.     

Two-color particle image velocimetry technique for an internal combustion engine

A two-color particle image velocimetry (PIV) technique has been applied to a single-cylinder motored research engine. Two-color PIV is a quantitative planar velocity measurement technique that can unambiguously determine the velocity magnitude and direction.

The work includes the development of an interrogation system, a series of computer simulations to determine the performance of the technique under various conditions, the comparison of these results to similar ones obtained for an autocorrelation PIV system, and a test of the technique by reconstructing the velocity field of a uniform jet flow.

The technique was then applied to the in-cylinder flow field of a motored single-cylinder, cup-in-head, research engine. A total of 27 instantaneous velocity fields were obtained at a single measurement plane for a single operating condition of the engine. The data were analyzed to yield ensemble-averaged velocity and velocity fluctuation.     

Water‐Splitting Electrocatalysis in Acid Conditions Using Ruthenate‐Iridate Pyrochlores

The pyrochlore solid solution (Na_0.33Ce_0.67)₂(Ir_1?xRu_x)₂O₇ (0≤x≤1), containing B‐site Ru^IV and Ir^IV is prepared by hydrothermal synthesis and used as a catalyst layer for electrochemical oxygen evolution from water at pH<7. The materials have atomically mixed Ru and Ir and their nanocrystalline form allows effective fabrication of electrode coatings with improved charge densities over a typical (Ru,Ir)O₂ catalyst. An in situ study of the catalyst layers using XANES spectroscopy at the Ir L_III and Ru K edges shows that both Ru and Ir participate in redox chemistry at oxygen evolution conditions and that Ru is more active than Ir, being oxidized by almost one oxidation state at maximum applied potential, with no evidence for ruthenate or iridate in +6 or higher oxidation states.     

Evidence of Noncentrosymmetry of Human Tooth Hydroxyapatite Crystals

Herein, we investigate human single hydroxyapatite crystals (enamel and dentine) by convergent‐beam electron diffraction (CBED) and automated electron‐diffraction tomography (ADT). The CBED pattern shows the absence of the mirror plane perpendicular to the c axis leading to the P6₃ space group instead of the P6₃/m space group considered for larger‐scale crystals, this is confirmed by ADT. This experimental evidence is of prime importance for understanding the morphogenesis and the architectural organization of calcified tissues.     

Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge

We continued prospective assessments of the Wilma–solvated interaction energy (SIE) platform for pose prediction, binding affinity prediction, and virtual screening on the challenging SAMPL4 data sets including the HIV-integrase inhibitor and two host–guest systems. New features of the docking algorithm and scoring function are tested here prospectively for the first time. Wilma–SIE provides good correlations with actual binding affinities over a wide range of binding affinities that includes strong binders as in the case of SAMPL4 host–guest systems. Absolute binding affinities are also reproduced with appropriate training of the scoring function on available data sets or from comparative estimation of the change in target’s vibrational entropy. Even when binding modes are known, SIE predictions lack correlation with experimental affinities within dynamic ranges below 2 kcal/mol as in the case of HIV-integrase ligands, but they correctly signaled the narrowness of the dynamic range. Using a common protein structure for all ligands can reduce the noise, while incorporating a more sophisticated solvation treatment improves absolute predictions. The HIV-integrase virtual screening data set consists of promiscuous weak binders with relatively high flexibility and thus it falls outside of the applicability domain of the Wilma–SIE docking platform. Despite these difficulties, unbiased docking around three known binding sites of the enzyme resulted in over a third of ligands being docked within 2 Å from their actual poses and over half of the ligands docked in the correct site, leading to better-than-random virtual screening results.