167 research outputs found
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
The pituri story: a review of the historical literature surrounding traditional Australian Aboriginal use of nicotine in Central Australia
The harmful outcomes of nicotine self administration have been the focus of sustained global health education campaigns that have targeted tobacco smoking and to a lesser extent, smokeless tobacco use. 'Smokeless tobacco' infers that the nicotine is not burnt, and administration can be through a range of methods including chewing. The chewing of wild tobacco plants (Nicotiana spp.) is practiced across a broad inland area of Central Australia by traditional Aboriginal groups. Collectively these plants are known by a variety of names - one common name being 'pituri'. This is the first paper to examine the historical literature and consider the linkage between pituri use and health outcomes. Using a narrative approach, this paper reviews the literature generated since 1770 surrounding the term pituri and the behaviours associated with its use. The review examines the scientific literature, as well as the diaries and journals of nineteenth century explorers, expedition notes, and early Australian novels to expound the scientific evidence and broaden the sense of understanding related to pituri, particularly the behavioural elements. The evaluation considers the complexities of ethnobotany pertaining to language and distance and the ethnopharmacology of indigenous plant usage. The review compares the use of burnt and smokeless tobacco to pituri and establishes the foundation for research into the clinical significance and health outcomes of pituri use. Additionally, this review provides contemporary information for clinicians providing care for patients who chew pituri
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
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
A level set simulation for ordering of quantum dots via cleaved-edge overgrowth
Cleaved-edge overgrowth (CEO) is a promising technique to obtain ordered arrays of quantum dots, where the size and position of the dots can be controlled very well. We present level set simulations for CEO. Our simulations illustrate how the quality of the CEO technique depends on the potential energy surface (PES) for adatom diffusion, and thus suggest how variations of the PES can potentially improve the uniformity of quantum dot arrays
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
YASA: yet another time series segmentation algorithm for anomaly detection in big data problems
Time series patterns analysis had recently attracted the attention of the research community for real-world applications. Petroleum industry is one of the application contexts where these problems are present, for instance for anomaly detection. Offshore petroleum platforms rely on heavy turbomachines for its extraction, pumping and generation operations. Frequently, these machines are intensively monitored by hundreds of sensors each, which send measurements with a high frequency to a concentration hub. Handling these data calls for a holistic approach, as sensor data is frequently noisy, unreliable, inconsistent with a priori problem axioms, and of a massive amount. For the anomalies detection problems in turbomachinery, it is essential to segment the dataset available in order to automatically discover the operational regime of the machine in the recent past. In this paper we propose a novel time series segmentation algorithm adaptable to big data problems and that is capable of handling the high volume of data involved in problem contexts. As part of the paper we describe our proposal, analyzing its computational complexity. We also perform empirical studies comparing our algorithm with similar approaches when applied to benchmark problems and a real-life application related to oil platform turbomachinery anomaly detection
Self-assembly of quantum dots: effect of neighbor islands on the wetting in coherent Stranski-Krastanov growth
The wetting of the homogeneously strained wetting layer by dislocation-free
three-dimensional islands belonging to an array has been studied. The array has
been simulated as a chain of islands in 1+1 dimensions. It is found that the
wetting depends on the density of the array, the size distribution and the
shape of the neighbor islands. Implications for the self-assembly of quantum
dots grown in the coherent Stranski-Krastanov mode are discussed.Comment: 4 pages, 6 figures, accepted version, minor change
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
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
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