Effectiveness and safety of secukinumab in 608 patients with psoriatic arthritis in real life: a 24-month prospective, multicentre study.

Objectives: To evaluate in a multicentric Italian cohort of patients with psoriatic arthritis (PsA) on secukinumab followed for 24 months: (1) the long-term effectiveness and safety of secukinumab, (2) the drug retention rate and minimal disease activity (MDA), (3) differences in the outcomes according to the biological treatment line: biologic-naïve patients () versus multifailure () patients.

Methods: Consecutive patients with PsA receiving secukinumab were evaluated prospectively. Disease characteristics, previous/ongoing treatments, comorbidities and follow-up duration were collected.

The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study.

In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130-350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics.

Molecular epizootiology and diagnosis of porcine babesiosis in Sardinia, Italy.

The recent characterization of the 18S ribosomal RNA (rRNA) of a pathogenic Babesia species in a domestic sow paved the way for establishing diagnostic and epidemiological tools for porcine babesiosis. Here, we developed the first specific Babesia sp. Suis PCR, and we applied this test to a panel of samples collected from animals living in a typical Mediterranean environment (Sardinia, Italy), including domestic pigs, wild boars, and ticks.

Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.

The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy.

Shortcomings of the standard Lennard-Jones dispersion term in water models, studied with force matching.

In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces.

Characterization of the Methane-Graphene Hydrophobic Interaction in Aqueous Solution from Ab Initio Simulations.

In this article, the interaction between a methane molecule and a graphene plane in liquid water has been characterized employing DFT-based free energy Molecular Dynamics calculations. This system represents a good model to understand the generic interaction between a small hydrophobic solute (methane molecule) and an extense hydrophobic surface (graphene plane). The structural and dynamical properties of graphene and methane hydration water are analyzed and found to be closely related to the main features of the potential of mean force.

Boundary based on exchange symmetry theory for multilevel simulations. II. Multiple time scale approach.

The QM/MM BEST method presented in the first article of this series [M. Shiga and M. Masia, J.

Boundary based on exchange symmetry theory for multilevel simulations. I. Basic theory.

In this paper, we lay the foundations for a new method that allows multilevel simulations of a diffusive system, i.e., a system where a flux of particles through the boundaries might disrupt the primary region.

Influence of site-dependent pigment-protein interactions on excitation energy transfer in photosynthetic light harvesting.

A site-dependent spectral density system-bath model of the Fenna-Matthews-Olsen (FMO) pigment-protein complex is developed using results from ground-state molecular mechanics simulations together with a partial charge difference model for how the long-range contributions to the chromophore excitation energies fluctuate with environmental configuration. A discussion of how best to consistently process the chromophore excitation energy fluctuation correlation functions calculated in these classical simulations to obtain reliable site-dependent spectral densities is presented. The calculations reveal that chromophores that are close to the protein-water interface can experience strongly dissipative environmental interactions characterized by reorganization energies that can be as much as 2-3 times those of chromophores that are buried deep in the hydrophobic protein scaffolding.

Estimating chloride polarizability in a water solution.

The evaluation of the hydrated chloride anion polarizability is hereby addressed by using density functional theory based calculations in the condensed phase. In this study, the quantum probability associated with maximally localized Wannier functions is included to account for the spatial extent of the electronic density. It is shown that the anion polarizability is not appreciably influenced upon solvation.

Unraveling the role of water in the stereoselective step of aqueous proline-catalyzed aldol reactions.

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self-condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First-principles molecular dynamics simulations were used to study the free-energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high-level static first-principles calculations were employed to characterize the transition states for microsolvated species.

Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field.

In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials.

Seroepidemiologic survey for Chlamydia suis in wild boar (Sus scrofa) populations in Italy.

We used serology to estimate the prevalence of exposure to chlamydiae in Italian populations of wild boars (Sus scrofa). Sera from 173 hunter-killed wild boars harvested during the 2006-2009 hunting seasons in three Italian regions were tested for antibodies to Chlamydia suis, Chlamydophila pecorum, Chlamydophila abortus, and Chlamydophila psittaci by the microimmunofluorescence test. Antibody titers to chlamydiae ≥ 1:32 were detected in 110 of the 173 samples tested (63.

Constructing simple yet accurate potentials for describing the solvation of HCl/water clusters in bulk helium and nanodroplets.

The infrared spectroscopy of molecules, complexes, and molecular aggregates dissolved in superfluid helium clusters, commonly called HElium NanoDroplet Isolation (HENDI) spectroscopy, is an established, powerful experimental technique for extracting high resolution ro-vibrational spectra at ultra-low temperatures. Realistic quantum simulations of such systems, in particular in cases where the solute is undergoing a chemical reaction, require accurate solute-helium potentials which are also simple enough to be efficiently evaluated over the vast number of steps required in typical Monte Carlo or molecular dynamics sampling. This precludes using global potential energy surfaces as often parameterized for small complexes in the realm of high-resolution spectroscopic investigations that, in view of the computational effort imposed, are focused on the intermolecular interaction of rigid molecules with helium.

Estimation of Partial Charges in Small Zeolite Imidazolate Frameworks from Density Functional Theory Calculations.

Zeolitic Imidazolate Frameworks (ZIFs) are the new frontier in the field of metal-organic materials. They incorporate the confining properties of the more traditional aluminosilicate zeolites together with the catalytic activity provided by transition metal ions and organic links. Computation of atomic point charges for these hybrid materials is important in the field of molecular simulations for substantial prediction of experimental results.

A molecular dynamics study and molecular level explanation of pressure dependence of ionic conductivity of potassium chloride in water.

Experimental ionic conductivity of different alkali ions in water shows markedly different dependences on pressure. Existing theories such as that of Hubbard-Onsager are unable to explain these dependences on pressure of the ionic conductivity for all ions. We report molecular dynamics investigation of potassium chloride solution at low dilution in water at several pressures between 1 bar and 2 kbar.

Aggregation-induced chemical reactions: acid dissociation in growing water clusters.

Understanding chemical reactivity at ultracold conditions, thus enabling molecular syntheses via interstellar and atmospheric processes, is a key issue in cryochemistry. In particular, acid dissociation and proton transfer reactions are ubiquitous in aqueous microsolvation environments. Here, the full dissociation of a HCl molecule upon stepwise solvation by a small number of water molecules at low temperatures, as relevant to helium nanodroplet isolation (HENDI) spectroscopy, is analyzed in mechanistic detail.

The polarizable point dipoles method with electrostatic damping: implementation on a model system.

Recently, the use of polarizable force fields in Molecular Dynamics simulations has been gaining importance, since they allow a better description of heterogeneous systems compared to simple point charges force fields. Among the various techniques developed in the last years the one based on polarizable point dipoles represents one of the most used. In this paper, we review the basic technical issues of the method, illustrating the way to implement intramolecular and intermolecular damping of the electrostatic interactions, either with and without the Ewald summation method.

Role of the reagents consumption in the chaotic dynamics of the Belousov-Zhabotinsky oscillator in closed unstirred reactors.

Chemical oscillations generated by the Belousov-Zhabotinsky reaction in batch unstirred reactors, show a characteristic chaotic transient in their dynamical regime, which is generally found between two periodic regions. Chemical chaos starts and finishes by following a direct and an inverse Ruelle-Takens-Newhouse scenario, respectively. In previous works we showed, both experimentally and theoretically, that the complex oscillations are generated by the coupling among the nonlinear kinetics and the transport phenomena, the latter due to concentration and density gradients.

Aggregation-induced dissociation of HCl(H2O)4 below 1 K: the smallest droplet of acid.

Acid dissociation and the subsequent solvation of the charged fragments at ultracold temperatures in nanoenvironments, as distinct from ambient bulk water, are relevant to atmospheric and interstellar chemistry but remain poorly understood. Here we report the experimental observation of a nanoscopic aqueous droplet of acid formed within a superfluid helium cluster at 0.37 kelvin.

On Ion and Molecular Polarization of Halides in Water.

The high polarizability of halide anions affects, in aqueous solutions, many phenomena ranging from hydrogen bond dynamics to water interfaces' structure. In this Letter dipolar interactions of halides in water are investigated through Car-Parrinello Molecular Dynamics simulations. Contrary to previous studies, a different polarization of first and second hydration shell water molecules is found.

Dynamical properties of confined water nanoclusters: Simulation study of hydrated zeolite NaA: structural and vibrational properties.

Water nanoclusters confined to zeolitic cavities have been extensively investigated by various experimental techniques. We report a series of molecular dynamics simulations at different temperatures and for water nanoclusters of different sizes in order to attempt an atomistic interpretation of the properties of these systems. The cavities of zeolite NaA are spherical in shape and about 1 nm in diameter and can host nanoclusters of water containing nearly up to 24 water molecules.

Bifurcations in spiral tip dynamics induced by natural convection in the Belousov-Zhabotinsky reaction.

The transition to spatial-temporal complexity exhibited by spiral waves under the effect of gravitational field in the Belousov-Zhabotinsky reaction is numerically studied on the basis of spiral tip dynamics. Successive transformations in tip trajectories are characterized as a function of the hydrodynamical parameter and attributed to a Ruelle-Takens-Newhouse scenario to chaos. The analysis describes the emergence of complexity in terms of the interplay between the evolution of the velocity field and concentration waves.