Search

We present a first-principles study of the structural, electronic, and optical properties of hydrogenated amorphous silicon (a-Si:H). To this end, atomic configurations of a-Si:H with 72 and 576 atoms respectively are generated using ab initio molecular dynamics, where the larger structures are defect free, closely matching the experimental situation and enabling the comparison of the electronic and optical properties with experimental results. Density functional theory calculations are applied to both configurations in order to obtain the electronic wave functions. These are analyzed and characterized with respect to their localization and their contribution to the density of states, and are used for calculating ab initio absorption spectra of a-Si:H. The results show that both the size and the defect structure of the configurations modify the electronic and optical properties and in particular the value of the band gap. This value could be improved by calculating quasi-particle (QP) corrections to the single-particle spectra using the G0W0 method. We find that the QP corrections can be described by a set of scissors shift parameters, which can also be used in calculations of larger structures. The analysis of individual contributions to the absorption by evaluating the optical matrix elements indicates that strong localization enhances the optical coupling, but has little effect on the average transition probability 〈 | v cv | 2 〉 , for which we find a dependence E 2 + const on the photon energy E, irrespective of the nature of the initial or final state.

The solubilization mechanism of lipid membranes in the presence of Triton X-100 (TX-100) is investigated at molecular resolution using molecular dynamics (MD) simulations. Thanks to the large time and length scales accessible by the hybrid particle-field formulation of the models employed here, the complex process of membrane solubilization has been studied, with the goal of verifying the three stage model reported in the literature. DPPC lipid bilayers and vesicles have been studied at different concentrations of the TX-100 detergent employing coarse grained (CG) models. Systems up to ∼600.000 beads, corresponding to more than 2 millions heavy atoms, have been simulated. Moreover, in order to clarify several experimental pieces of evidence, both slow and fast detergent partition scenarios have been investigated. Flat and curved (vesicles) lipid bilayer surfaces, interacting with TX-100, have been considered to study the curvature effects on the detergent partition rate in the membrane. Shape and conformational changes of mixed DPPC/TX-100 vesicles, as a function of TX-100 content, have also been studied. In particular, high curvature surfaces, corresponding to a higher local TX-100 content, promote a membrane rupture. In flat lipid surfaces, on the time scale simulated the detergent partition is almost absent, following a different pathway of the solubilization membrane mechanism. © 2017 the Owner Societies.

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 Young's 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.

The structural properties of amorphous SiSe 2 are studied by performing extensive first-principle molecular dynamics simulations. Comparison with experiments in terms of total neutron scattering factor and nuclear magnetic resonance data confirms the reliability of our model. Partial pair correlation functions and ring statistics are used to identify the structural units whose spatial organization gives raise to the intermediate range order. An accurate analysis reveals that amorphous SiSe 2 is largely a chemically ordered system consisting mainly of a network of silicon centered tetrahedra. Different types of connections among the tetrahedra can be identified and classified. In particular edge-sharing connections seem to play a fundamental role in the establishment of the intermediate range order and in the appearance of the first sharp diffraction peak in the total neutron scattering factor.

Arg, Lys and Asp amino acids are known to play a critical role in the adhesion of the RKLPDA engineered peptide on the (101) surface of the titania anatase phase. To understand their contribution to peptide adhesion, we have considered the relevant charge states due to protonation (Arg and Lys) or deprotonation (Asp) occurring in neutral water solution, and studied their adsorption on the (101) anatase TiO2 surface by ab initio total energy calculations based on density functional theory. The adsorption configurations on the hydrated surface are compared to those on the dry surface considering also the presence of the hydration shell around amino acid side-chains. This study explains how water molecules mediate the adsorption of charged amino acids showing that protonated amino acids are chemically adsorbed much more strongly than de-protonated Asp. Moreover it is shown that the polar screening of the hydration shell reduces the adsorption energy of the protonated amino acids to a small extent, thus evidencing that both Arg and Lys strongly adhere on the (101) anatase TiO2 surface in neutral water solution and that they play a major role in the adhesion of the RKLPDA peptide.

The structural properties of liquid SiSe 2 are studied by using first-principles molecular dynamics simulations. A comparative analysis involving liquid GeSe 2 is carried out by focusing on partial pair correlation functions and coordination numbers. Both systems are characterized by intermediate range order. However, chemical order is more enhanced in liquid SiSe 2 than in liquid GeSe 2 , leading to a larger percentage of AX 4 tetrahedra and a smaller number of homopolar bonds.

First-principles molecular dynamics simulations are carried out to study the structural properties of liquid SiSe2. This system is a prototype of disordered network-forming material characterized by intermediate range order, i.e. structural order involving distances well beyond nearest neighbors. Our simulations show that the atomic structure is chemically ordered, with most of the Si atoms fourfold coordinated in SiSe4 tetrahedra. The resulting population of Si sites, established in terms of connectivity among tetrahedra, is in good agreement with experimental predictions.

Short-range order and static atomic displacement parameters, previously determined from diffuse neutron scattering for Ni-8.9 at.% Al equilibrated at 775 K and quenched to room temperature, were used to study lattice relaxation effects in molecular-dynamics simulations. An occupation of average lattice sites with Ni and Al atoms compatible with the short-range ordered state was taken as the starting situation. Displacement parameters obtained from the relaxation simulations and from diffuse neutron scattering show general similarity in magnitude and dependence on distance. Also, the species dependence of the displacement parameters known from diffuse X-ray scattering investigations is reproduced in magnitude.

The thermodynamic behavior of the carbon schwarzite face-centered cubic (fcc)-(C 36 ) 2 has been investigated via semi-empirical tight-binding molecular dynamics (TBMD) simulations up to and above the mechanical instability temperature ( T ≃4000 K) where the system transforms into a planar graphitic-like structure. The thermal variation of the structure stability has been monitored via the analysis of the order of connection (OC) parameter k c as a function of temperature and of the vacancy concentration. The structure and the properties of the highest temperature phase have been also characterized.

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.

Structures of amorphous silicon have been generated by using a suitable implementation of the reverse Monte Carlo technique, based on the reproduction of different experimental data. The structures have been subsequently relaxed at fixed temperature and pressure via tight binding molecular dynamics. The amorphous structures have been further characterized by evaluating structural, dynamic and electronic structure properties, as a function of temperature, up to and above the melting point. The model of amorphous silicon undergoes a melting transition at Tal≃0.55Tm (where Tm is the homogeneous melting temperature of the bulk crystal). In the temperature range between Tal and Tm, the system exhibits thermodynamic and structural properties typical of an undercooled liquid.

We elucidate the structural properties of amorphous ${\mathrm{S}\mathrm{i}\mathrm{S}\mathrm{e}}_{2}$ by first-principles molecular dynamics. The calculated structure factor is in very good agreement with experiments, as well as the number of corner- and edge-sharing tetrahedra. By focusing on the sequences of Si atoms linked via intra- and intertetrahedral bonds, we identify the predominant structural motifs. The sequences involving both corner- and edge-sharing connections are significantly more frequent than those formed exclusively by edge-shared Si atoms. Our results clarify a longstanding controversy on the structure of this prototypical disordered network-forming material.

Molecular Dynamics simulations in the Tight-Binding approach allow the study of the ionic and electronic structures of semiconductors. The Tight-Binding codes are characterized by inhomogeneous data distribution and require the repeated diagonalization of a large sparse matrix to compute the whole body of its eigenvalues and eigenvectors. We describe the porting of this code on a parallel computer: we show the parallelization strategy for both the Molecular Dynamics part of the code and for the diagonalization needed at each time step. The parallelization has been carried out within the High Performance Fortran (HPF) environment, and tested on IBM SP architectures. The integration of optimized parallel mathematical routines is also described.

We show that tight-binding molecular dynamics provides a detailed description of the relations between structural deformations and changes in the electronic features during a Jahn-Teller process. In this case the metal-semiconductor displacitive phase transition occurring in epitaxial FeSi2 with film thickness can be correctly reproduced and interpreted by variable cell molecular dynamics for the bulk configuration. We show that it actually corresponds to a pattern of local Jahn-Teller distortions occurring at selected sites in different times, so that the configurational evolution cannot be described by a global coordinate.

A genetic algorithm for the optimization of the ground-state structure of a metallic cluster has been developed and ported on a SIMD–MIMD parallel platform. The SIMD part of the parallel platform is represented by a Quadrics/APE100 consisting of 512 floating point units, while the MIMD part is formed by a cluster of workstations. The proposed algorithm is composed by a part where the genetic operators are applied to the elements of the population and a part which performs a further local relaxation and the fitness calculation via Molecular Dynamics. These parts have been implemented on the MIMD and on the SIMD part, respectively. Results have been compared to those generated by using Simulated Annealing.

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.

An atomic-scale structure of amorphous silicon, generated by reverse Monte Carlo, has been used as a starting configuration for finite temperature molecular dynamics simulations performed by an orthogonal tight binding Hamiltonian. Structural, dynamic, elastic and electronic structure properties have been investigated in the range of temperatures up to and above the melting transition. The amorphous silicon structure undergoes a melting transition at a temperature sensibly smaller than that of the crystalline structure. Above this temperature, the structure has the same properties of an under-cooled liquid and it has a metallic behavior.