Evolutionary approach for finding the atomic structure of steps on stable crystal surfaces

The problem addressed here can be concisely formulated as follows: Given a stable surface orientation with a known reconstruction and given a direction in the plane of this surface, find the atomic structure of the steps oriented along that direction. We report a robust and generally applicable variable-number genetic algorithm for determining the atomic configuration of crystallographic steps, and exemplify it by finding structures for several types of monatomic steps on Si(114)-2×1. We show that the location of the step edge with respect to the terrace reconstructions, the step width (number of atoms), and the positions of the atoms in the step region can all be simultaneously determined

The stability of strained H:Si(105) and H:Ge(105) surfaces

We report atomic scale studies of the effect of applied strain and hydrogen environment on the reconstructions of the (105) Si and Ge surfaces. Surface energy calculations for monohydride-terminated (001) and (105) reconstructions reveal that the recently established single-height rebonded model is unstable not only with respect to (001), but also in comparison to other monohydride (105) structures. This finding persists for both Si and Ge, for applied biaxial strains from -4% to 4%, and for nearly the entire relevant domain of the chemical potential of hydrogen, thus providing an explanation for the recently observed H-induced destabilization of the Ge(105) surface

The incomplete beta function law for parallel tempering sampling of classical canonical systems

We show that the acceptance probability for swaps in the parallel tempering Monte Carlo method for classical canonical systems is given by a universal function that depends on the average statistical fluctuations of the potential and on the ratio of the temperatures. The law, called the incomplete beta function law, is valid in the limit that the two temperatures involved in swaps are close to one another. An empirical version of the law, which involves the heat capacity of the system, is developed and tested on a Lennard-Jones cluster. We argue that the best initial guess for the distribution of intermediate temperatures for parallel tempering is a geometric progression and we also propose a technique for the computation of optimal temperature schedules. Finally, we demonstrate that the swap efficiency of the parallel tempering method for condensed-phase systems decreases naturally to zero at least as fast as the inverse square root of the dimensionality of the physical system.Comment: 11 pages, 4 figures; minor changes; to appear in J. Chem. Phy

Strain induced stabilization of stepped Si and Ge surfaces near (001)

We report on calculations of the formation energies of several [100] and [110] oriented step structures on biaxially stressed Si and Ge (001) surfaces. It is shown that a novel rebonded [100] oriented single-height step is strongly stabilized by compressive strain compared to most well-known step structures. We propose that the side walls of ``hut''-shaped quantum dots observed in recent experiments on SiGe/Si films are made up of these steps. Our calculations provide an explanation for the nucleationless growth of shallow mounds, with steps along the [100] and [110] directions in low- and high-misfit films, respectively, and for the stability of the (105) facets under compressive strain.Comment: to appear in Appl. Phys. Lett.; v2=minor corrections,figs resize

Modelling Cell Cycle using Different Levels of Representation

Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform computerised simulations of biological systems, which are called in silico experiments, to attain important insights and predictions about the system behaviour with a considerably lower cost. Computer visualisation is an important part of this approach, since it provides a realistic representation of the system behaviour. We define a formal methodology to model biological systems using different levels of representation: a purely formal representation, which we call molecular level, models the biochemical dynamics of the system; visualisation-oriented representations, which we call visual levels, provide views of the biological system at a higher level of organisation and are equipped with the necessary spatial information to generate the appropriate visualisation. We choose Spatial CLS, a formal language belonging to the class of Calculi of Looping Sequences, as the formalism for modelling all representation levels. We illustrate our approach using the budding yeast cell cycle as a case study

Orientation-dependent binding energy of graphene on palladium

Using density functional theory calculations, we show that the binding strength of a graphene monolayer on Pd(111) can vary between physisorption and chemisorption depending on its orientation. By studying the interfacial charge transfer, we have identified a specific four-atom carbon cluster that is responsible for the local bonding of graphene to Pd(111). The areal density of such clusters varies with the in-plane orientation of graphene, causing the binding energy to change accordingly. Similar investigations can also apply to other metal substrates, and suggests that physical, chemical, and mechanical properties of graphene may be controlled by changing its orientation.Comment: 5 pages, 6 figure