Toward a DFT-based molecular dynamics description of Co(II) binding in sulfur-rich peptides

In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules. Benchmark calculations are performed on [Co(Cys-H)]+ and [Co(Glutathione-H)]+ complexes, since they are the main fragments of the Co(II)-Cys and Co(II)-glutathione systems found in gas phase electrospray ionisation mass spectrometry (ESI-MS) experiments done in our laboratory. We also present benchmark calculations on the [Co(H2O)6)]2+ cluster with direct comparisons to highly correlated ab initio calculations and experiments. In particular, we investigated the dissociation path of one water molecule from the first hydration shell of Co(II) with CPMD. Overall, our molecular dynamics simulations shed some light on the nature of the Co(II) interaction and reactivity in Co(II)-phytochelatin building block systems related to the biological and environmental activity of the metal, either in the gas or liquid phase.     

Controllability of quasi-linear Hamiltonian NLS equations

We prove internal controllability in arbitrary time, for small data, for quasi-linear Hamiltonian NLS equations on the circle. We use a procedure of reduction to constant coefficients up to order zero and HUM method to prove the controllability of the linearized problem. Then we apply a Nash–Moser–Hörmander implicit function theorem as a black box.     

Existence and multiplicity of solutions for elliptic equations with jumping nonlinearities

In this paper we are concerned with a semilinear elliptic Dirichlet problem with jumping nonlinearity and, using a completely variational method, we show that the number of solutions may be arbitrarily large provided the number of jumped eigenvalues is large enough. In order to prove this fact, we show that for every positive integer k, when a suitable parameter is large enough, there exists a solution which presents k peaks. Under the assumptions we consider in this paper, new (unexpected) phenomena are observed in the study of this problem and new methods are required to construct the k-peaks solutions and describe their asymptotic behavior (weak limits of the rescaled solutions, localization of the concentration points of the peaks, asymptotic profile of the rescaled peaks, etc.).     

Multigram scale, solventless, and diffusion-controlled route to highly monodisperse PbS nanocrystals

High-quality PbS nanocrystals were produced in multigram-scale quantities through a solventless, heterogeneous, and relatively green route. The heterogeneous nature of this reaction allows one to limit the diffusion in the system, allowing for unprecedented monodispersity and quality of the product demonstrated by a full-width at half-maximum of the photoluminescence peak (PL fwhm) as low as 52 meV, a Stokes shift as low as 10 meV, and a quantum yield (QY) of 40%. The growth of the nanocrystals is interpreted in the framework of a diffusion-controlled Ostwald growth in conditions of strong supersaturation.     

Froc: a new fluorous protective group for peptide and oligosaccharide synthesis

[STRUCTURE: SEE TEXT] The synthesis of a new fluorous protecting group, Froc, is described. This new fluorous tag has been used in peptide and carbohydrate synthesis by our group and readily allows us to fully characterize each product (NMR, MS) and monitor each synthetic step by TLC. Purification of the products is generally performed by standard fluorous solid-phase extraction techniques (e.g., F-SPE), but standard chromatographic purifications are also possible if required.     

Clustering of financial time series

This paper addresses the topic of classifying financial time series in a fuzzy framework proposing two fuzzy clustering models both based on GARCH models. In general clustering of financial time series, due to their peculiar features, needs the definition of suitable distance measures. At this aim, the first fuzzy clustering model exploits the autoregressive representation of GARCH models and employs, in the framework of a partitioning around medoids algorithm, the classical autoregressive metric. The second fuzzy clustering model, also based on partitioning around medoids algorithm, uses the Caiado distance, a Mahalanobis-like distance, based on estimated GARCH parameters and covariances that takes into account the information about the volatility structure of time series. In order to illustrate the merits of the proposed fuzzy approaches an application to the problem of classifying 29 time series of Euro exchange rates against international currencies is presented and discussed, also comparing the fuzzy models with their crisp version.     

Personalized Metabolic Profile by Synergic Use of NMR and HRMS

A new strategy that takes advantage of the synergism between NMR and UHPLC–HRMS yields accurate concentrations of a high number of compounds in biofluids to delineate a personalized metabolic profile (SYNHMET). Metabolite identification and quantification by this method result in a higher accuracy compared to the use of the two techniques separately, even in urine, one of the most challenging biofluids to characterize due to its complexity and variability. We quantified a total of 165 metabolites in the urine of healthy subjects, patients with chronic cystitis, and patients with bladder cancer, with a minimum number of missing values. This result was achieved without the use of analytical standards and calibration curves. A patient’s personalized profile can be mapped out from the final dataset’s concentrations by comparing them with known normal ranges. This detailed picture has potential applications in clinical practice to monitor a patient’s health status and disease progression.     

An efficient simulation algorithm for the generalized von Mises distribution of order two

In this article we propose an exact efficient simulation algorithm for the generalized von Mises circular distribution of order two. It is an acceptance-rejection algorithm with a piecewise linear envelope based on the local extrema and the inflexion points of the generalized von Mises density of order two. We show that these points can be obtained from the roots of polynomials and degrees four and eight, which can be easily obtained by the methods of Ferrari and Weierstrass. A comparative study with the von Neumann acceptance-rejection, with the ratio-of-uniforms and with a Markov chain Monte Carlo algorithms shows that this new method is generally the most efficient.     

Ab initio pseudopotential study of vacancies and self-interstitials in hcp titanium

By means of an ab initio plane-wave pseudopotential method, monovacancy, divacancy and self-interstitials in hcp titanium are investigated. The calculated monovacancy formation energy is 1.97 eV, which is in excellent agreement with other theoretical calculations, and agrees qualitatively with published experimental results. The relaxation of the atoms around a single vacancy is observed to be small. Two divacancy configurations, the in-plane and the off-plane, have also been shown to be equally stable. With regards to the interstitials, of the eight configurations studied, two (octahedral and basal octahedral) have relatively lower formation energies and are, thus, the most likely stable configurations. We find small energy differences between them, suggesting their possible co-existence. It is also observed that the tetrahedral configuration decays to a split dumbbell configuration, whereas both the basal tetrahedral and the basal pseudocrowdion interstitials decay to the basal octahedral configuration. Using the nudged elastic band method (NEB), we determine a possible minimum energy path (MEP) for the diffusion of self-interstitial titanium atoms from an octahedral site to the nearest octahedral site. The energy barrier for this migration mechanism is shown to be about 0.20 eV.