101,410 research outputs found
Compositional uniformity, domain patterning and the mechanism underlying nano-chessboard arrays
We propose that systems exhibiting compositional patterning at the nanoscale,
so far assumed to be due to some kind of ordered phase segregation, can be
understood instead in terms of coherent, single phase ordering of minority
motifs, caused by some constrained drive for uniformity. The essential features
of this type of arrangements can be reproduced using a superspace construction
typical of uniformity-driven orderings, which only requires the knowledge of
the modulation vectors observed in the diffraction patterns. The idea is
discussed in terms of a simple two dimensional lattice-gas model that simulates
a binary system in which the dilution of the minority component is favored.
This simple model already exhibits a hierarchy of arrangements similar to the
experimentally observed nano-chessboard and nano-diamond patterns, which are
described as occupational modulated structures with two independent modulation
wave vectors and simple step-like occupation modulation functions.Comment: Preprint. 11 pages, 11 figure
The EM Algorithm and the Rise of Computational Biology
In the past decade computational biology has grown from a cottage industry
with a handful of researchers to an attractive interdisciplinary field,
catching the attention and imagination of many quantitatively-minded
scientists. Of interest to us is the key role played by the EM algorithm during
this transformation. We survey the use of the EM algorithm in a few important
computational biology problems surrounding the "central dogma"; of molecular
biology: from DNA to RNA and then to proteins. Topics of this article include
sequence motif discovery, protein sequence alignment, population genetics,
evolutionary models and mRNA expression microarray data analysis.Comment: Published in at http://dx.doi.org/10.1214/09-STS312 the Statistical
Science (http://www.imstat.org/sts/) by the Institute of Mathematical
Statistics (http://www.imstat.org
Equi-energy sampler with applications in statistical inference and statistical mechanics
We introduce a new sampling algorithm, the equi-energy sampler, for efficient
statistical sampling and estimation. Complementary to the widely used
temperature-domain methods, the equi-energy sampler, utilizing the
temperature--energy duality, targets the energy directly. The focus on the
energy function not only facilitates efficient sampling, but also provides a
powerful means for statistical estimation, for example, the calculation of the
density of states and microcanonical averages in statistical mechanics. The
equi-energy sampler is applied to a variety of problems, including exponential
regression in statistics, motif sampling in computational biology and protein
folding in biophysics.Comment: This paper discussed in: [math.ST/0611217], [math.ST/0611219],
[math.ST/0611221], [math.ST/0611222]. Rejoinder in [math.ST/0611224].
Published at http://dx.doi.org/10.1214/009053606000000515 in the Annals of
Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical
Statistics (http://www.imstat.org
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