Computational prediction of L_{3} EXAFS spectra of gold nanoparticles from classical molecular dynamics simulations

We present a computational approach for the simulation of extended x-ray absorption fine structure (EXAFS) spectra of nanoparticles directly from molecular dynamics simulations without fitting any of the structural parameters of the nanoparticle to experimental data. The calculation consists of two stages. First, a molecular dynamics simulation of the nanoparticle is performed and then the EXAFS spectrum is computed from “snapshots” of structures extracted from the simulation. A probability distribution function approach calculated directly from the molecular dynamics simulations is used to ensure a balanced sampling of photoabsorbing atoms and their surrounding scattering atoms while keeping the number of EXAFS calculations that need to be performed to a manageable level. The average spectrum from all configurations and photoabsorbing atoms is computed as an Au L3-edge EXAFS spectrum with the FEFF 8.4 package, which includes the self-consistent calculation of atomic potentials. We validate and apply this approach in simulations of EXAFS spectra of gold nanoparticles with sizes between 20 and 60 Å. We investigate the effect of size, structural anisotropy, and thermal motion on the gold nanoparticle EXAFS spectra and we find that our simulations closely reproduce the experimentally determined spectra

Diffuse degassing of carbon dioxide on the NW sector of Colli Albani volcanic complex (Rome, Italy)

Systematic CO2 soil flux surveys at Cava dei Selci on the Colli Albani volcano (28 seasonal surveys since the year 2000) have shown a significant variation of diffuse CO2 release, with a marked decrease, from 25 to 4 tonnes/day, from May 2000 to August 2004, followed by a new increase. Over the same period, CO2 flux halved at S. Maria delle Mole (16.8 tonnes/day in 2000 and 8.3 tonnes/day in 2006). Also the quantity of CO2 dissolved in the deep waters of the Albano crater lake decreased by one order of magnitude in the period 1997-2006. The high CO2 flux values in 2000 could represent the “tail” of a strong degassing episode recorded at Colli Albani in 1995 and related to local earthquakes. The following decrease of CO2 flux could reflect a permeability decrease caused by hydrothermal calcite precipitation favored by PCO2 reduction in the deep sourc

Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations

Water models with realistic physical-chemical properties are essential to study a variety of biomedical processes or engineering technologies involving molecules or nanomaterials. Atomistic models of water are constrained by the feasible computational capacity, but calibrated coarse-grained (CG) ones can go beyond these limits. Here, we compare three popular atomistic water models with their corresponding CG model built using finite-size particles such as ellipsoids. Differently from previous approaches, short-range interactions are accounted for with the generalized Gay-Berne potential, while electrostatic and long-range interactions are computed from virtual charges inside the ellipsoids. Such an approach leads to a quantitative agreement between the original atomistic models and their CG counterparts. Results show that a timestep of up to 10 fs can be achieved to integrate the equations of motion without significant degradation of the physical observables extracted from the computed trajectories, thus unlocking a significant acceleration of water-based mesoscopic simulations at a given accuracy

Epac as a novel effector of airway smooth muscle relaxation

Dysfunctional regulation of airway smooth muscle tone is a feature of obstructive airway diseases such as asthma and chronic obstructive pulmonary disease. Airway smooth muscle contraction is directly associated with changes in the phosphorylation of myosin light chain (MLC), which is increased by Rho and decreased by Rac. Although cyclic adenosine monophosphate (cAMP)-elevating agents are believed to relieve bronchoconstriction mainly via activation of protein kinase A (PKA), here we addressed the role of the novel cAMP-mediated exchange protein Epac in the regulation of airway smooth muscle tone. Isometric tension measurements showed that specific activation of Epac led to relaxation of guinea pig tracheal preparations pre-contracted with methacholine, independently of PKA. In airway smooth muscle cells, Epac activation reduced methacholine-induced MLC phosphorylation. Moreover, when Epac was stimulated, we observed a decreased methacholine-induced RhoA activation, measured by both stress fibre formation and pull-down assay whereas the same Epac activation prevented methacholine-induced Rac1 inhibition measured by pull-down assay. Epac-driven inhibition of both methacholine-induced muscle contraction by Toxin B-1470, and MLC phosphorylation by the Rac1-inhibitor NSC23766, were significantly attenuated, confirming the importance of Rac1 in Epac-mediated relaxation. Importantly, human airway smooth muscle tissue also expresses Epac, and Epac activation both relaxed pre-contracted human tracheal preparations and decreased MLC phosphorylation. Collectively, we show that activation of Epac relaxes airway smooth muscle by decreasing MLC phosphorylation by skewing the balance of RhoA/Rac1 activation towards Rac1. Therefore, activation of Epac may have therapeutical potential in the treatment of obstructive airway diseases

Wettability of soft PLGA surfaces predicted by experimentally augmented atomistic models

A challenging topic in surface engineering is predicting the wetting properties of soft interfaces with different liquids. However, a robust computational protocol suitable for predicting wettability with molecular precision is still lacking. In this article, we propose a workflow based on molecular dynamics simulations to predict the wettability of polymer surfaces and test it against the experimental contact angle of several polar and nonpolar liquids, namely water, formamide, toluene, and hexane. The specific case study addressed here focuses on a poly(lactic-co-glycolic acid) (PLGA) flat surface, but the proposed experimental-modeling protocol may have broader fields of application. The structural properties of PLGA slabs have been modeled on the surface roughness determined with microscopy measurements, while the computed surface tensions and contact angles were validated against standardized characterization tests, reaching a discrepancy of less than 3% in the case of water. Overall, this work represents the initial step toward an integrated multiscale framework for predicting the wettability of more complex soft interfaces, which will eventually take into account the effect of surface topology at higher scales and synergically be employed with experimental characterization techniques