Surface molecular dynamics simulation with two orthogonal surface steps: how to beat the particle conservation problem

Due to particle conservation, Canonical Molecular Dynamics (MD) simulations fail in the description of surface phase transitions involving coverage or lateral density changes. However, a step on the surface can act effectively as a source or a sink of atoms, in the simulation as well as in real life. A single surface step can be introduced by suitably modifying planar Periodic Boundary Conditions (PBC), to accommodate the generally inequivalent stacking of two adjacent layers. We discuss here how, through the introduction of two orthogonal surface steps, particle number conservation may no longer represent a fatal constraint for the study of these surface transitions. As an example, we apply the method for estimating temperature-induced lateral density increase of the reconstructed Au (001) surface; the resulting anisotropic cell change is consistent with experimental observations. Moreover, we implement this kind of scheme in conjunction with the variable curvature MD method, recently introduced by our group.Comment: 9 pages, 5 figures, accepted for publication in Surface Science (ECOSS-19

A Generic Model of Contracts for Embedded Systems

We present the mathematical foundations of the contract-based model developed in the framework of the SPEEDS project. SPEEDS aims at developing methods and tools to support "speculative design", a design methodology in which distributed designers develop different aspects of the overall system, in a concurrent but controlled way. Our generic mathematical model of contract supports this style of development. This is achieved by focusing on behaviors, by supporting the notion of "rich component" where diverse (functional and non-functional) aspects of the system can be considered and combined, by representing rich components via their set of associated contracts, and by formalizing the whole process of component composition

Islands, craters, and a moving surface step on a hexagonally reconstructed (100) noble metal surface

Deposition/removal of metal atoms on the hex reconstructed (100) surface of Au, Pt and Ir should present intriguing aspects, since a new island implies hex -> square deconstruction of the substrate, and a new crater the square -> hex reconstruction of the uncovered layer. To obtain a microscopic understanding of how islands/craters form in these conditions, we have conducted simulations of island and crater growth on Au(100), whose atomistic behavior, including the hex reconstruction on top of the square substrate, is well described by mean s of classical many-body forces. By increasing/decreasing the Au coverage on Au(100), we find that island/craters will not grow unless they exceed a critical size of about 8-10 atoms. This value is close to that which explains the nonlinear coverage dependence observed in molecular adsorption on the closely related surface Pt (100). This threshold size is rationalized in terms of a transverse step correlation length, measuring the spatial extent where reconstruction of a given plane is disturbed by the nearby step.Comment: 11 pages, 5 figures, accepted for publication in Surface Science (ECOSS-18

Escaping free-energy minima

We introduce a novel and powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of a coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates.A characteristic feature of this dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the free energy surface, allowing the efficient exploration and accurate determination of the free energy surface as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.Comment: 3 figure

Realistic simulations of Au(100): Grand Canonical Monte Carlo and Molecular Dynamics

The large surface density changes associated with the (100) noble metals surface hex-reconstruction suggest the use of non-particle conserving simulation methods. We present an example of a surface Grand Canonical Monte Carlo applied to the transformation of a square non reconstructed surface to the hexagonally covered low temperature stable Au(100). On the other hand, classical Molecular Dynamics allows to investigate microscopic details of the reconstruction dynamics, and we show, as an example, retraction of a step and its interplay with the surface reconstruction/deconstruction mechanism.Comment: 9 pages, 5 figures, accepted for publication in Surf. Rev. and Letters (ICSOS-6

Realistic grand canonical Monte Carlo surface simulation: application to Ar(111)

Most realistic, off-lattice surface simulations are done canonically--- conserving particles. For some applications, however, such as studying the thermal behavior of rare gas solid surfaces, these constitute bad working conditions. Surface layer occupancies are believed to change with temperature, particularly at preroughening, and naturally call for a grand canonical approach, where particle number is controlled by a chemical potential. We report preliminary results of novel realistic grand canonical Monte Carlo simulations of the Lennard-Jones (LJ) fcc(111) surface, believed to represent a quantitative model of e.g. Ar(111). The results are successful and highly informative for temperatures up to roughly 0.8 T_m, where clear precursor signals of preroughening are found. At higher temperatures, convergence to equilibrium is hampered by large fluctuations.Comment: 4 pages, REVTeX, 3 PostScript figure

Ab initio simulations of the Ag(111)/Al2O3 interface at intermediate oxygen partial pressures

The relative stability of different realizations of the Ag(111)/Alumina interfaces with varying oxygen partial pressures is investigated by means of ab initio density functional theory (DFT) simulations. Previous theoretical studies of similar systems always involve oversimplified geometries like stoichiometric Al-terminated, Al-rich, or O-terminated alumina interfaces. Such framework cannot explain the experimental behavior observed at intermediate oxygen partial pressure. Our approach, instead, suggests that the oxygen at the interface can play an important role at intermediate concentrations, leading to a more realistic interpretation of the experimental dat

Bent surface free energy differences from simulation

We present a calculation of the change of free energy of a solid surface upon bending of the solid. It is based on extracting the surface stress through a molecular dynamics simulation of a bent slab by using a generalized stress theorem formula, and subsequent integration of the stress with respect to strain as a function of bending curvature. The method is exemplified by obtaining and comparing free energy changes with curvature of various reconstructed Au(001) surfaces.Comment: 14 pages, 2 figures, accepted for publication in Surface Science (ECOSS-19

Modeling a distributed Heterogeneous Communication System using Parametric Timed Automata

In this report, we study the application of the Parametric Timed Automata(PTA) tool to a concrete case of a distributed Heterogeneous Communication System (HCS). The description and requirements of HCS are presented and the system modeling is explained carefully. The system models are developed in UPPAAL and validated by different test cases. Part of the system models are then converted into parametric timed automata and the schedulability checking is run to produce the schedulability regions