246 research outputs found
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 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 atoms exhibits scaling in the form
\mbox{)} where 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 , where is the
stationary adatom density in the presence of a constant flux. The probability
that nucleation occurs at time after the deposition of the second
adatom, decays for short time as a power law [] in and
logarithmically [] in ; for long time it decays
exponentially. Theories of the nucleation rate based on the assumption
that it is proportional to are shown to overestimate 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)
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