Fulvio Ciriaco

Stochastic simulations of mixed-lipid compartments: from self-assembling vesicles to self-producing protocells.

The computational platform ENVIRONMENT, developed to simulate stochastically reaction systems in varying compartmentalized conditions [Mavelli and Ruiz-Mirazo: Philos Trans R Soc Lond B Biol Sci 362:1789-1802, 2007; Physical Biology 7(3): 036002, 2010], is here applied to study the dynamic properties and stability of model protocells that start producing their own lipid molecules (e.g., phospholipids), which get inserted in previously self-assembled vesicles, made of precursor amphiphiles (e.g., fatty acids). Attention is mainly focused on the changes that this may provoke in the permeability of the compartment, as well as in its eventual osmotic robustness.

Semiquinone oscillations as a tool for investigating the ubiquinone binding to photosynthetic reaction centers.

Semiquinone oscillations induced by light pulses in the presence of exogenous electron donors are a valuable source of information on the kinetics and thermodynamics of ubiquinone chemistry relevant to the QB site of the photosynthetic reaction center (RC). In previous attempts to achieve the quantitative interpretation of data, the ubiquinone concentration was considered constant during the experiment since it was much bigger than that of RC. In this work, we extended existing models to low ubiquinone concentrations revealing several hidden processes taking place during the ubiquinone photoreduction and enabling the evaluation of the ubiquinone binding constant KQ at the QB site. The proposed approach provides for the first time the evaluation of KQ without any preliminary treatment of ubiquinone extraction from the binding site, thereby better preserving its native structure.

DISORDERED SURFACES : A SMOOTHED HE-TARGET SCATTERING POTENTIAL FOR METAL ATOMS ADSORBED ON METAL SURFACES

Abstract The theoretical interpretation of experimental results on He scattering from metal adatoms epitaxially grown on metal substrates makes use, in general, of an interaction potential that, as far as the He-adatom interaction is concerned, is a pairwise sum of Lennard-Jones ( V LJ ) terms. This approach results in more corrugated metal surfaces than expected on the basis of both experimental data and qualitative considerations on the contribution of the electron densities of the metal adatoms to the repulsive part of the interaction potential. The present work suggests a very simple way to significantly reduce or eliminate the surface corrugation by averaging the He-adsorbate potential over a unit cell of the substrate lattice. The so obtained potential ( V AV ) was compared with V LJ for the HeAg/Pt(111) colliding system on the basis of turning point surfaces, specular and diffractive intensities vs. surface coverage and angular intensity distribution of scattered atoms, calculated under the sudden approximation. These data show that V AV , although too simple to correctly reproduce all the features of the He-adatom interaction, could represent a useful tool in the study of the growth of metal adlayers.

The correlation between the statistical properties of surface defect distribution and the specular intensity obtained from low energy He scattering technique

Abstract This paper shows that the He diffraction specular intensity does not depend in a simple, predictable way on single statistical parameters describing the surface defect lateral distribution. In particular it shows the lack of correlation between specular intensity and the geometrical overlap of single defect cross sections, a parameter widely used in the literature for a qualitative interpretation of He atom diffraction data. An approach to the problem of surface structure determination is attempted on the basis of a cluster expansion of the scattering matrix at reflection angle.

Azetidine–Borane Complexes: Synthesis, Reactivity, and Stereoselective Functionalization

The present study reports, for the first time, the synthesis and structural features of azetidine-borane complexes, as well as their reactivity in lithiation reactions. A temperature-dependent stereoselectivity has been disclosed in the reaction of borane with N-alkyl-2-arylazetidines, allowing for a stereoselective preparation of azetidine-borane complexes 2 and 3. A regioselective hydrogen/lithium permutation, at the benzylic position, was observed in lithiation reactions of complexes possessing a syn relationship, between the ring proton and the BH3 group. In contrast, scarce or no reactivity was noticed in complexes lacking such a stereochemical requirement. The configurational stability of the lithiated intermediates has also been investigated, in order to shed some light on the stereoselectivity of the lithiation/electrophile trapping sequence. Calculations helped in supporting experimental observations, concerning structure and reactivity of these azetidine-borane complexes. Data suggest that the BH3 group could promote the lithiation reaction likely by an electrostatic complex induced proximity effect. Interestingly, a new synthetic strategy for the synthesis of N-alkyl-2,2-disubstituted azetidines has been developed.

Light particle scattering diffraction from surfaces in the sudden approximation

The sudden approximation can be the foundation of a code for performing inexpensive calculations on light particle scattering from huge surface systems. The paper describes the mathematical framework and a sample code which can be used to perform sudden calculations either in the semiclassical approximation or in an exact numerical approach. Also a straightforward extension to the treatment of inelastic collisions in a discrete set of excited states is derived and implemented.

Order and disorder signatures in the specular scattering intensity of He particles from adsorbate covered Pt surfaces

Abstract Simulated specular scattering intensity of He particles from Xe and CO adsorbed on Pt surfaces shows distinctive features of the surface order parameters which are, however, not observed in experiments. Inferences may be drawn about the influence of long-range order on the scattering properties.

A program for the solution of chemical equilibria among multiple phases

We present a program for the calculation of concentrations at chemical equilibrium in systems with one or more phases. We explain the main difficulties that such a program must surmount and the strategies that were devised for the present one, comparing them to others that can be found in the literature.

He scattering from disordered surfaces: specular intensity, cross-section and surface structure

Abstract Since the specular intensity and scattering matrix are related by a quadratical relation, a term is present in the intensity which scales as the square of the defect surface coverage. One can directly account for the term in every calculation which provides the scattering matrix. The explicit formulas under the sudden approximation are reported and their implications discussed. Any relation between cross-section and specular intensity which does not take it into account is demonstrated to be inadequate even at very low coverage values. Consequently cross-sections calculated on phenomenological grounds cannot give correct information on surface structure.