Massimo Celino

Atomic hydrogen adsorption on a Stone–Wales defect in graphite

Abstract Ab initio electronic structure calculations have been used to evaluate the binding energy of atomic hydrogen to graphite lattice defects. Results show that carbon sites belonging to a Stone–Wales defect are preferred binding sites with respect to undefected sites. Upon hydrogen adsorption, carbon sites undergo a sizeable tetragonalization effect which is more pronounced on the defected sizes.

Atomic-Scale Modeling of the Interaction between Short Polypeptides and Carbon Surfaces

We performed a comparative study of the adsorption of an in vitro selected peptide on two different carbon surfaces: a flat graphene and a curved (0,15) nanotube. The sequence was selected from recent experiments, as the one giving the highest carbon affinity for carbon nanotubes. Rigid docking of the molecule on the two surfaces by a genetic algorithm was followed by molecular dynamics simulations with empirical force fields (OPLS-AA) in water at finite temperature. The total free energies of folding and adhesion and the quality of surface binding were determined, based on a combination of solvation energy, formation of hydrogen bonds, and amount of the apolar (hydrophobic) contact surface between peptide and carbon surface. For both cases, we find a strong adhesion energy and large nonpolar contact surface. Isoleucines and tryptophans are the most strongly bound residues to the two carbon surfaces, the latter one largely dominating. In the case of the carbon nanotube, the peptide shows several competing stable structures, corresponding to different possible molecular foldings, and a propensity to enhance the intramolecular stability by forming new hydrogen bonds. In both systems, different arrangements of the histidine and tryptophan residues enable a better adaptation to the carbon surfaces. These findings suggest that the experimentally observed surface specificity of the peptide on nanotubes may depend on its capability to support multiple strongly bound configurations.

Strain maps at the atomic scale below Ge pyramids and domes on a Si substrate

In this letter, the strain field below uncapped Ge islands of a different shape on a Si(001) substrate is estimated by molecular dynamics simulations at a realistic scale. Comparison to the Fourier transform maps of transmission electron micrographs, recently reported in literature, shows a very good agreement. We point out that the complex deformation in silicon, just below the edges of the Ge islands, is far from being uniaxial. The stress distribution generated by such a strain determines the range of interdot repulsion.

Atomistic simulation of liquid lead and lead–bismuth eutectic

Abstract Lead and the Pb–Bi eutectic (Pb 55.9 at.%) have been modeled by a n -body potential derived from a second moment approximation of a tight binding Hamiltonian. The thermal behavior of the two systems in the liquid phase has been reproduced and relevant structural parameters have been evaluated and compared with experimental data. The diffusion coefficients and the activation energy for diffusion have been also evaluated.

Self-Assembly of Triton X-100 in Water Solutions: A Multiscale Simulation Study Linking Mesoscale to Atomistic Models

A multiscale scheme is proposed and validated for Triton X-100 (TX-100), which is a detergent widely employed in biology. The hybrid particle field formulation of the model allows simulations of large-scale systems. The coarse-grained (CG) model, accurately validated in a wide range of concentrations, shows a critical micelle concentration, shape transition in isotropic micellar phase, and appearance of hexagonal ordered phase in the experimental ranges reported in the literature. The fine resolution of the proposed CG model allows one to obtain, by a suitable reverse mapping procedure, atomistic models of micellar assemblies and of the hexagonal phase. In particular, atomistic models of the micelles give structures in good agreement with experimental pair distance distribution functions and hydrodynamic measurements. The picture emerging by detailed analysis of simulated systems is quite complex. Polydisperse mixtures of spherical-, oblate-, and prolate-shaped aggregates have been found. The shape and the micelle behavior are mainly dictated by the aggregation number (Nagg). Micelles with low Nagg values (∼40) are spherical, while those with high Nagg values (∼140 or larger) are characterized by prolate ellipsoidal shapes. For intermediate Nagg values (∼70), fluxional micelles alternating between oblate and prolate shapes are found. The proposed model opens the way to investigations of several mechanisms involving TX-100 assembly in protein and membrane biophysics.

Neutral and anionic CuO2 : an ab inito study

Abstract By using first-principles calculations within density functional theory via the local density approximation (LDA) and the generalized-gradient approximation (GGA) of Perdew and Wang for exchange and correlation, we calculate the equilibrium structures of CuO 2 and CuO 2 − clusters. In the case of CuO 2 , three isomers (OCuO linear and two CuO 2 complexes, side-on and bent) lie within 0.5 eV, while the negatively charged cluster is most stable as a linear molecule. Our assignment of measured photo-electron spectra features on the basis of the electronic density of states (EDOS) suggests that the bent structure is the most stable among the two forms of CuO 2 − complexes.

Point defects and stacking faults in TiSi2 phases by tight binding molecular dynamics

Tight binding molecular dynamics is used to predict the structure and the total energy of the most relevant intrinsic point defects in C54 and C49 TiSi2. The comparison between the relative formation energies of point defects of the two phases in contact with a Si substrate suggests that the metastable C49 form has a higher concentration of point defects. In particular, we point out that Si vacancies and (010) stacking faults should be quite common in the C49 structure. This issue could be important in explaining the kinetic advantage of the latter phase in film growth by solid state reaction.

Crystal-Like Rearrangements of Icosahedra in Simulated Copper-Zirconium Metallic Glasses and their Effect on Mechanical Properties

Indications of the Cu2Zr Laves phase are observed in MD simulations of amorphous Cu64Zr36 upon isothermal holding just above the glass transition temperature. The structural evolution towards Cu2Zr is accompanied by an increase in the fraction of Cu-centered icosahedra, which demonstrates that a large icosahedral fraction does not just indicate structural relaxation. The crystal-like regions generate an increase in strength and Youngs modulus, and a stronger localized shear band. A universal relation between the fraction of full icosahedra and their interconnectivity is found, and both can be modified simultaneously via changes of temperature or strain.

On the effect of quench rate on the structure of amorphous carbon

Abstract We have simulated, via tight binding molecular dynamics (TBMD), the process of the quench from a melt of an atomic scale system of carbon. We have correlated the local properties of the resulting structure to the quench rate used to bring the liquid phase beyond the glass transition temperature. Results have been analyzed also in terms of the hamiltonian model used to describe the simulated system. In this respect, amorphous structures generated via tight binding and ab initio molecular dynamics have been compared. Results indicate that quench rates as slow as 1014 K/s produce the onset of an increasingly high fraction of threefold coordinated sites in the structure. Moreover, it has been put in evidence the tendency of the tight binding approach to favor threefold coordinated sites with respect to fourfold coordinated, even in the fast quench rates domain.

Molecular dynamics of ionic self-diffusion at an MgO grain boundary

AbstractThe characterization of self-diffusion in MgO grain boundaries is a materials science problem of general interest, being relevant to the stability and reactivity of MgO layers in artificial nanostructures as well as to the understanding of mass transport and morphological evolution in polycrystalline metal oxides which are employed in many technological applications. In addition, atomic transport in MgO is a key factor to describe the rheology of the Earth’s lower mantle. In this work, we tackle the problem using a classical molecular dynamics model and finite-temperature simulations. To this purpose, we first design a stable grain boundary structure, which is meant to be representative of general internal interfaces in nanocrystalline MgO. The Mg and O self-diffusion coefficients along this grain boundary are then determined as a function of temperature by calculating the mean-square ionic displacement in the boundary region. Two different diffusion regimes at low and high temperature are identified, allowing to obtain the relevant activation enthalpies for migration from the temperature dependance of the diffusion coefficients. Our results prove that Mg diffusion along MgO grain boundaries is sufficiently fast to explain the recently reported development of MgO hollow structures during repeated hydrogen sorption cycles in Mg/MgO nanoparticles.