Scaling of Heteroepitaxial Island Sizes

Monte Carlo simulations of an atomistic solid-on-solid model are used to study the effect of lattice misfit on the distribution of two-dimensional islands sizes as a function of coverage $\Theta$ in the submonolayer aggregation regime of epitaxial growth. Misfit promotes the detachment of atoms from the perimeter of large pseudomorphic islands and thus favors their dissolution into smaller islands that relieve strain more efficiently. The number density of islands composed of $s$ atoms exhibits scaling in the form \mbox{$N_s(\Theta) \sim \Theta / \langle s \rangle^2 \, g(s/\langle s \rangle$)} where $\langle s \rangle$ is the average island size. Unlike the case of homoepitaxy, a rate equation theory based on this observation leads to qualitatively different behavior than observed in the simulations.Comment: 10 pages, LaTeX 2.09, IC-DDV-94-00

Level Set Approach to Reversible Epitaxial Growth

We generalize the level set approach to model epitaxial growth to include thermal detachment of atoms from island edges. This means that islands do not always grow and island dissociation can occur. We make no assumptions about a critical nucleus. Excellent quantitative agreement is obtained with kinetic Monte Carlo simulations for island densities and island size distributions in the submonolayer regime.Comment: 7 pages, 9 figure

Submonolayer Epitaxy Without A Critical Nucleus

The nucleation and growth of two--dimensional islands is studied with Monte Carlo simulations of a pair--bond solid--on--solid model of epitaxial growth. The conventional description of this problem in terms of a well--defined critical island size fails because no islands are absolutely stable against single atom detachment by thermal bond breaking. When two--bond scission is negligible, we find that the ratio of the dimer dissociation rate to the rate of adatom capture by dimers uniquely indexes both the island size distribution scaling function and the dependence of the island density on the flux and the substrate temperature. Effective pair-bond model parameters are found that yield excellent quantitative agreement with scaling functions measured for Fe/Fe(001).Comment: 8 pages, Postscript files (the paper and Figs. 1-3), uuencoded, compressed and tarred. Surface Science Letters, in press

Web-based visualisation of the transcriptional control network of Escherichia coli

Transcription is one of the basic processes of gene expression, controlled by a complex network of biochemical reactions. Despite its importance, most work on the visualisation of biochemical networks focuses on the representation of metabolic pathways. The visualisation of the complex networks controlling transcription requires the implementation of a hierarchical approach that allows the display of the structure of each regulatory region with its transcription factors and regulated operons. This paper presents a web-based application for the visualisation of transcriptional control networks. It takes as case study the organism Escherichia coli. The definition of the visual components implemented is mainly based on those proposed by Shen-Orr et al., 2002, slightly extended to visualise complex networks. © 2004 - IOS Press and Bioinformation Systems e.V. and the authors. All rights reserved. [accessed 2014 October 15

Magic Islands and Barriers to Attachment: A Si/Si(111)7x7 Growth Model

Surface reconstructions can drastically modify growth kinetics during initial stages of epitaxial growth as well as during the process of surface equilibration after termination of growth. We investigate the effect of activation barriers hindering attachment of material to existing islands on the density and size distribution of islands in a model of homoepitaxial growth on Si(111)7x7 reconstructed surface. An unusual distribution of island sizes peaked around "magic" sizes and a steep dependence of the island density on the growth rate are observed. "Magic" islands (of a different shape as compared to those obtained during growth) are observed also during surface equilibration.Comment: 4 pages including 5 figures, REVTeX, submitted to Physical Review

Epitaxial Growth Kinetics with Interacting Coherent Islands

The Stranski-Krastanov growth kinetics of undislocated (coherent) 3-dimensional islands is studied with a self-consistent mean field rate theory that takes account of elastic interactions between the islands. The latter are presumed to facilitate the detachment of atoms from the islands with a consequent decrease in their average size. Semi-quantitative agreement with experiment is found for the time evolution of the total island density and the mean island size. When combined with scaling ideas, these results provide a natural way to understand the often-observed initial increase and subsequent decrease in the width of the coherent island size distribution.Comment: 4 pages, 4 figure

Implication of the overlap representation for modelling generalized parton distributions

Based on a field theoretically inspired model of light-cone wave functions, we derive valence-like generalized parton distributions and their double distributions from the wave function overlap in the parton number conserved s-channel. The parton number changing contributions in the t-channel are restored from duality. In our construction constraints of positivity and polynomiality are simultaneously satisfied and it also implies a model dependent relation between generalized parton distributions and transverse momentum dependent parton distribution functions. The model predicts that the t-behavior of resulting hadronic amplitudes depends on the Bjorken variable x_Bj. We also propose an improved ansatz for double distributions that embeds this property.Comment: 15 pages, 8 eps figure

Spatio-temporal distribution of nucleation events during crystal growth

We consider irreversible second-layer nucleation that occurs when two adatoms on a terrace meet. We solve the problem analytically in one dimension for zero and infinite step-edge barriers, and numerically for any value of the barriers in one and two dimensions. For large barriers, the spatial distribution of nucleation events strongly differs from $\rho^2$, where $\rho$ is the stationary adatom density in the presence of a constant flux. The probability $Q(t)$ that nucleation occurs at time $t$ after the deposition of the second adatom, decays for short time as a power law [$Q(t)\sim t^{-1/2}$] in $d=1$ and logarithmically [$Q(t)\sim 1/\ln(t/t_0)$] in $d=2$; for long time it decays exponentially. Theories of the nucleation rate $\omega$ based on the assumption that it is proportional to $\rho^2$ are shown to overestimate $\omega$ by a factor proportional to the number of times an adatom diffusing on the terrace visits an already visited lattice site.Comment: 4 pages, 3 figures; accepted for publication on PR

Strain-Dependence of Surface Diffusion: Ag on Ag(111) and Pt(111)

Using density-functional theory with the local-density approximation and the generalized gradient approximation we compute the energy barriers for surface diffusion for Ag on Pt(111), Ag on one monolayer of Ag on Pt(111), and Ag on Ag(111). The diffusion barrier for Ag on Ag(111) is found to increase linearly with increasing lattice constant. We also discuss the reconstruction that has been found experimentally when two Ag layers are deposited on Pt(111). Our calculations explain why this strain driven reconstruction occurs only after two Ag layers have been deposited.Comment: 4 pages, 3 figures, Phys. Rev. B 55 (1997), in pres

mGene.web: a web service for accurate computational gene finding

We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to train the system with their own data for other organisms on the push of a button, a functionality that will greatly accelerate the annotation of newly sequenced genomes. The system is built in a highly modular way, such that individual components of the framework, like the promoter prediction tool or the splice site predictor, can be used autonomously. The underlying gene finding system mGene is based on discriminative machine learning techniques and its high accuracy has been demonstrated in an international competition on nematode genomes. mGene.web is available at http://www.mgene.org/web, it is free of charge and can be used for eukaryotic genomes of small to moderate size (several hundred Mbp)