Structural role of counterions adsorbed on self-assembled peptide nanotubes

Among noncovalent forces, electrostatic ones are the strongest and possess a rather long-range action. For these reasons, charges and counterions play a prominent role in self-assembly processes in water and therefore in many biological systems. However, the complexity of the biological media often hinders a detailed understanding of all the electrostatic-related events. In this context, we have studied the role of charges and counterions in the self-assembly of lanreotide, a cationic octapeptide. This peptide spontaneously forms monodisperse nanotubes (NTs) above a critical concentration when solubilized in pure water. Free from any screening buffer, we assessed the interactions between the different peptide oligomers and counterions in solutions, above and below the critical assembly concentration. Our results provide explanations for the selection of a dimeric building block instead of a monomeric one. Indeed, the apparent charge of the dimers is lower than that of the monomers because of strong chemisorption. This phenomenon has two consequences: (i) the dimer-dimer interaction is less repulsive than the monomer-monomer one and (ii) the lowered charge of the dimeric building block weakens the electrostatic repulsion from the positively charged NT walls. Moreover, additional counterion condensation (physisorption) occurs on the NT wall. We furthermore show that the counterions interacting with the NTs play a structural role as they tune the NTs diameter. We demonstrate by a simple model that counterions adsorption sites located on the inner face of the NT walls are responsible for this size control.     

Structured probabilistic inference

Probabilistic inference is among the main topics with reasoning in uncertainty in AI. For this purpose, Bayesian Networks (BNs) is one of the most successful and efficient Probabilistic Graphical Model (PGM) so far. Since the mid-90s, a growing number of BNs extensions have been proposed. Object-oriented, entity-relationship and first-order logic are the main representation paradigms used to extend BNs. While entity-relationship and first-order models have been successfully used for machine learning in defining lifted probabilistic inference, object-oriented models have been mostly underused. Structured inference, which exploits the structural knowledge encoded in an object-oriented PGM, is a surprisingly unstudied technique. In this paper we propose a full object-oriented framework for PRM and propose two extensions of the state-of-the-art structured inference algorithm: SPI which removes the major flaws of existing algorithms and SPISBB which largely enhances SPI by using d-separation.     

Synergetic effect of host-guest chemistry and spin crossover in 3D Hofmann-like metal-organic frameworks [Fe(bpac)M(CN)4] (M=Pt, Pd, Ni)

The synthesis and characterization of a series of three‐dimensional (3D) Hofmann‐like clathrate porous metal–organic framework (MOF) materials [Fe(bpac)M(CN)₄] (M=Pt, Pd, and Ni; bpac=bis(4‐pyridyl)acetylene) that exhibit spin‐crossover behavior is reported. The rigid bpac ligand is longer than the previously used azopyridine and pyrazine and has been selected with the aim to improve both the spin‐crossover properties and the porosity of the corresponding porous coordination polymers (PCPs). The 3D network is composed of successive {Fe[M(CN)₄]}_n planar layers bridged by the bis‐monodentate bpac ligand linked in the apical positions of the iron center. The large void between the layers, which represents 41.7 % of the unit cell, can accommodate solvent molecules or free bpac ligand. Different synthetic strategies were used to obtain a range of spin‐crossover behaviors with hysteresis loops around room temperature; the samples were characterized by magnetic susceptibility, calorimetric, Mössbauer, and Raman measurements. The complete physical study reveals a clear relationship between the quantity of included bpac molecules and the completeness of the spin transition, thereby underlining the key role of the π–π stacking interactions operating between the host and guest bpac molecules within the network. Although the inclusion of the bpac molecules tends to increase the amount of active iron centers, no variation of the transition temperature was measured. We have also investigated the ability of the network to accommodate the inclusion of molecules other than water and bpac and studied the synergy between the host–guest interaction and the spin‐crossover behavior. In fact, the clathration of various aromatic molecules revealed specific modifications of the transition temperature. Finally, the transition temperature and the completeness of the transition are related to the nature of the metal associated with the iron center (Ni, Pt, or Pd) and also to the nature and the amount of guest molecules in the lattice.     

NMR and pattern recognition methods in metabolomics: From data acquisition to biomarker discovery: A review

Metabolomics is the discipline where endogenous and exogenous metabolites are assessed, identified and quantified in different biological samples. Metabolites are crucial components of biological system and highly informative about its functional state, due to their closeness to functional endpoints and to the organism's phenotypes. Nuclear Magnetic Resonance (NMR) spectroscopy, next to Mass Spectrometry (MS), is one of the main metabolomics analytical platforms. The technological developments in the field of NMR spectroscopy have enabled the identification and quantitative measurement of the many metabolites in a single sample of biofluids in a non-targeted and non-destructive manner. Combination of NMR spectra of biofluids and pattern recognition methods has driven forward the application of metabolomics in the field of biomarker discovery. The importance of metabolomics in diagnostics, e.g. in identifying biomarkers or defining pathological status, has been growing exponentially as evidenced by the number of published papers. In this review, we describe the developments in data acquisition and multivariate analysis of NMR-based metabolomics data, with particular emphasis on the metabolomics of Cerebrospinal Fluid (CSF) and biomarker discovery in Multiple Sclerosis (MScl).     

Conformational effect on small angle neutron scattering behavior of interacting polyelectrolyte solutions: a perspective of integral equation theory

We present small angle neutron scattering (SANS) measurements of deuterium oxide (D(2)O) solutions of linear and star sodium poly(styrene sulfonate) (NaPSS) as a function of polyelectrolyte concentration. Emphasis is on understanding the dependence of their SANS coherent scattering cross section I(Q) on the molecular architecture of single polyelectrolyte. The key finding is that for a given concentration, star polyelectrolytes exhibit more pronounced characteristic peaks in I(Q), and the position of the first peak occurs at a smaller Q compared to their linear counterparts. Based on a model of integral equation theory, we first compare the SANS experimental I(Q) of salt-free polyelectrolyte solutions with that predicted theoretically. Having seen their satisfactory qualitative agreement, the dependence of counterion association behavior on polyelectrolyte geometry and concentration is further explored. Our predictions reveal that the ionic environment of polyelectrolyte exhibits a strong dependence on polyelectrolyte geometry at lower polyelectrolyte concentration. However, when both linear and star polyelectrolytes exceed their overlap concentrations, the spatial distribution of counterion is found to be essentially insensitive to polyelectrolyte geometry due to the steric effect.     

Analysis and reconstruction of a pulsed jet in crossflow by multi-plane snapshot POD

In this work, snapshot proper orthogonal decomposition (POD) is used to study a pulsed jet in crossflow where the velocity fields are extracted from stereoscopic particle image velocimetry (SPIV) results. The studied pulsed jet is characterized by a frequency f = 1 Hz, a Reynolds number Re _j  = 500 (based on the mean jet velocity ${\overline{U}_{j}}$  = 1.67 cm/s and a mean velocity ratio of R = 1). Pulsed jet and continuous jet are compared via mean velocity field trajectory and Q criterion. POD results of instantaneous, phase-averaged and fluctuating velocity fields are presented and compared in this paper. Snapshot POD applied on one plane allows us to distinguish an organization of the first spatial eigenmodes. A distinction between “natural modes” and “pulsed modes” is achieved with the results obtained by the pulsed and unforced jet. Secondly, the correlation tensor is established with four parallel planes (multi-plane snapshot POD) for the evaluation of volume spatial modes. These resulting modes are interpolated and the volume velocity field is reconstructed with a minimal number of modes for all the times of the pulsation period. These reconstructions are compared to orthogonal measurements to the transverse jet in order to validate the obtained three-dimensional velocity fields. Finally, this POD approach for the 3D flow field reconstruction from experimental data issued from planes parallel to the flow seems capable to extract relevant information from a complex three-dimensional flow and can be an alternative to tomo-PIV for large volume of measurement.     

On Pseudo-Riemannian Manifolds Whose Ricci Tensor is Parallel

Ricci-parallel Riemannian manifolds have a diagonal Ricci endomorphism Ric and are therefore, at least locally, a product of Einstein manifolds. This fails in the pseudo-Riemannian case. Using, on the one side, a general result in linear algebra due to Klingenberg and on the other side, a theorem on the holonomy of pseudo-Riemannian manifolds, this work classifies the different types of pseudo-Riemannian manifolds whose Ricci tensor is parallel.     

Multi-State Second-Order Nonlinear Optical Switches Incorporating One to Three Benzazolo-Oxazolidine Units: A Quantum Chemistry Investigation

This contribution employs quantum chemistry methods to describe the variations of the second nonlinear optical responses of molecular switches based on benzazolo-oxazolidine (BOX) units, connected by π-linkers, along their successive opening/closing. Under the fully closed forms, all of them display negligible first hyperpolarizability (β) values. When one BOX is opened, which is sketched as C→O, a push–pull π-conjugated segment is formed, having the potential to enhance β and to set the depolarization ratio (DR) to its one-dimensional-like value (DR = 5). This is observed when only one BOX is open, either for the monoBOX species (C→O) or for the diBOX (CC→CO) and triBOX (CCC→CCO) compounds, i.e., when the remaining BOXs stay closed. The next BOX openings have much different effects. For the diBOXs, the second opening (CO→OO) is associated with a decrease of β, and this decrease is tuned by controlling the conformation of the π-linker, i.e., the centrosymmetry of the whole compound because β vanishes in centrosymmetric compounds. For the triBOXs, the second opening gives rise to a Λ-shape compound, with a negligible change of β, but a decrease of the DR whereas, along the third opening, β remains similar and the DR decreases to the typical value of octupolar systems (DR = 1.5).     

Sweeping process with regular and nonregular sets

Differential inclusions involving the normal cone to a moving set are investigated. A special attention is paid to the sweeping process associated with sets for which no regularity assumption is required.     

Rearrangement of a mesylate tropane intermediate in nucleophilic substitution reactions. Synthesis of aza-bicyclo[3.2.1]octane and aza-bicyclo[3.2.2]nonane ethers,imides, and amines

Nucleophilic substitution of 2beta-mesyloxymethyl-N-methyl-3beta-p-tolyl-tropane intermediate with alkoxides, metal imides, or amines was found to lead not only to the expected bicyclo[3.2.1]octane (tropane) ether, imide, and amine derivatives but also to unexpected bicyclo[3.2.2]nonane derivatives. When alkoxides were used as nucleophile, only the rearranged bicyclo[3.2.2]nonane structure was obtained, whereas the use of amines or imides as nucleophile afforded a mixture of the two structures. The bicyclo[3.2.2]nonane structure was assigned by NMR analysis.