90 research outputs found
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
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
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
Effect of strain on surface diffusion in semiconductor heteroepitaxy
We present a first-principles analysis of the strain renormalization of the
cation diffusivity on the GaAs(001) surface. For the example of
In/GaAs(001)-c(4x4) it is shown that the binding of In is increased when the
substrate lattice is expanded. The diffusion barrier \Delta E(e) has a
non-monotonic strain dependence with a maximum at compressive strain values (e
0) studied.
We discuss the consequences of spatial variations of both the binding energy
and the diffusion barrier of an adatom caused by the strain field around a
heteroepitaxial island. For a simplified geometry, we evaluate the speed of
growth of two coherently strained islands on the GaAs(001) surface and identify
a growth regime where island sizes tend to equalize during growth due to the
strain dependence of surface diffusion.Comment: 10 pages, 8 figures, LaTeX2e, to appear in Phys. Rev. B (2001). Other
related publications can be found at
http://www.rz-berlin.mpg.de/th/paper.htm
Asymptotic Capture-Number and Island-Size Distributions for One-Dimensional Irreversible Submonolayer Growth
Using a set of evolution equations [J.G. Amar {\it et al}, Phys. Rev. Lett.
{\bf 86}, 3092 (2001)] for the average gap-size between islands, we calculate
analytically the asymptotic scaled capture-number distribution (CND) for
one-dimensional irreversible submonolayer growth of point islands. The
predicted asymptotic CND is in reasonably good agreement with kinetic
Monte-Carlo (KMC) results and leads to a \textit{non-divergent asymptotic}
scaled island-size distribution (ISD). We then show that a slight modification
of our analytical form leads to an analytic expression for the asymptotic CND
and a resulting asymptotic ISD which are in excellent agreement with KMC
simulations. We also show that in the asymptotic limit the self-averaging
property of the capture zones holds exactly while the asymptotic scaled gap
distribution is equal to the scaled CND.Comment: 4 pages, 1 figure, submitted to Phys. Rev.
The effect of monomer evaporation on a simple model of submonolayer growth
We present a model for thin film growth by particle deposition that takes
into account the possible evaporation of the particles deposited on the
surface. Our model focuses on the formation of two-dimensional structures. We
find that the presence of evaporation can dramatically affect the growth
kinetics of the film, and can give rise to regimes characterized by different
``growth'' exponents and island size distributions. Our results are obtained by
extensive computer simulations as well as through a simple scaling approach and
the analysis of rate equations describing the system. We carefully discuss the
relationship of our model with previous studies by Venables and Stoyanov of the
same physical situation, and we show that our analysis is more general.Comment: 41 pages including figures, Revtex, to be published in Physical
Review
Coherent Stranski-Krastanov growth in 1+1 dimensions with anharmonic interactions: An equilibrium study
The formation of coherently strained three-dimensional islands on top of the
wetting layer in Stranski-Krastanov mode of growth is considered in a model in
1+1 dimensions accounting for the anharmonicity and non-convexity of the real
interatomic forces. It is shown that coherent 3D islands can be expected to
form in compressed rather than in expanded overlayers beyond a critical lattice
misfit. In the latter case the classical Stranski-Krastanov growth is expected
to occur because the misfit dislocations can become energetically favored at
smaller island sizes. The thermodynamic reason for coherent 3D islanding is the
incomplete wetting owing to the weaker adhesion of the edge atoms. Monolayer
height islands with a critical size appear as necessary precursors of the 3D
islands. The latter explains the experimentally observed narrow size
distribution of the 3D islands. The 2D-3D transformation takes place by
consecutive rearrangements of mono- to bilayer, bi- to trilayer islands, etc.,
after exceeding the corresponding critical sizes. The rearrangements are
initiated by nucleation events each next one requiring to overcome a lower
energetic barrier. The model is in good qualitative agreement with available
experimental observations.Comment: 12 pages text, 15 figures, Accepted in Phys.Rev.B, Vol.61, No2
Ab initio atomistic thermodynamics and statistical mechanics of surface properties and functions
Previous and present "academic" research aiming at atomic scale understanding
is mainly concerned with the study of individual molecular processes possibly
underlying materials science applications. Appealing properties of an
individual process are then frequently discussed in terms of their direct
importance for the envisioned material function, or reciprocally, the function
of materials is somehow believed to be understandable by essentially one
prominent elementary process only. What is often overlooked in this approach is
that in macroscopic systems of technological relevance typically a large number
of distinct atomic scale processes take place. Which of them are decisive for
observable system properties and functions is then not only determined by the
detailed individual properties of each process alone, but in many, if not most
cases also the interplay of all processes, i.e. how they act together, plays a
crucial role. For a "predictive materials science modeling with microscopic
understanding", a description that treats the statistical interplay of a large
number of microscopically well-described elementary processes must therefore be
applied. Modern electronic structure theory methods such as DFT have become a
standard tool for the accurate description of individual molecular processes.
Here, we discuss the present status of emerging methodologies which attempt to
achieve a (hopefully seamless) match of DFT with concepts from statistical
mechanics or thermodynamics, in order to also address the interplay of the
various molecular processes. The new quality of, and the novel insights that
can be gained by, such techniques is illustrated by how they allow the
description of crystal surfaces in contact with realistic gas-phase
environments.Comment: 24 pages including 17 figures, related publications can be found at
http://www.fhi-berlin.mpg.de/th/paper.htm
Self-diffusion of adatoms, dimers, and vacancies on Cu(100)
We use ab initio static relaxation methods and semi-empirical
molecular-dynamics simulations to investigate the energetics and dynamics of
the diffusion of adatoms, dimers, and vacancies on Cu(100). It is found that
the dynamical energy barriers for diffusion are well approximated by the
static, 0 K barriers and that prefactors do not depend sensitively on the
species undergoing diffusion. The ab initio barriers are observed to be
significantly lower when calculated within the generalized-gradient
approximation (GGA) rather than in the local-density approximation (LDA). Our
calculations predict that surface diffusion should proceed primarily via the
diffusion of vacancies. Adatoms are found to migrate most easily via a jump
mechanism. This is the case, also, of dimers, even though the corresponding
barrier is slightly larger than it is for adatoms. We observe, further, that
dimers diffuse more readily than they can dissociate. Our results are discussed
in the context of recent submonolayer growth experiments of Cu(100).Comment: Submitted to the Physical Review B; 15 pages including postscript
figures; see also http://www.centrcn.umontreal.ca/~lewi
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