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

Influence of adatom interactions on second layer nucleation

We develop a theory for the inclusion of adatom interactions in second layer nucleation occurring in epitaxial growth. The interactions considered are due to ring barriers between pairs of adatoms and binding energies of unstable clusters. The theory is based on a master equation, which describes the time development of microscopic states that are specified by cluster configurations on top of an island. The transition rates are derived by scaling arguments and tested against kinetic Monte-Carlo simulations. As an application we reanalyze experiments to determine the step edge barrier for Ag/Pt(111).Comment: 4 pages, 4 figure

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

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

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

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)

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)

The process of irreversible nucleation in multilayer growth. II. Exact results in one and two dimensions

We study irreversible dimer nucleation on top of terraces during epitaxial growth in one and two dimensions, for all values of the step-edge barrier. The problem is solved exactly by transforming it into a first passage problem for a random walker in a higher-dimensional space. The spatial distribution of nucleation events is shown to differ markedly from the mean-field estimate except in the limit of very weak step-edge barriers. The nucleation rate is computed exactly, including numerical prefactors.Comment: 22 pages, 10 figures. To appear in Phys. Rev.

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

A Hybrid Monte Carlo Method for Surface Growth Simulations

We introduce an algorithm for treating growth on surfaces which combines important features of continuum methods (such as the level-set method) and Kinetic Monte Carlo (KMC) simulations. We treat the motion of adatoms in continuum theory, but attach them to islands one atom at a time. The technique is borrowed from the Dielectric Breakdown Model. Our method allows us to give a realistic account of fluctuations in island shape, which is lacking in deterministic continuum treatments and which is an important physical effect. Our method should be most important for problems close to equilibrium where KMC becomes impractically slow.Comment: 4 pages, 5 figure