33,843 research outputs found
Node similarity within subgraphs of protein interaction networks
We propose a biologically motivated quantity, twinness, to evaluate local
similarity between nodes in a network. The twinness of a pair of nodes is the
number of connected, labeled subgraphs of size n in which the two nodes possess
identical neighbours. The graph animal algorithm is used to estimate twinness
for each pair of nodes (for subgraph sizes n=4 to n=12) in four different
protein interaction networks (PINs). These include an Escherichia coli PIN and
three Saccharomyces cerevisiae PINs -- each obtained using state-of-the-art
high throughput methods. In almost all cases, the average twinness of node
pairs is vastly higher than expected from a null model obtained by switching
links. For all n, we observe a difference in the ratio of type A twins (which
are unlinked pairs) to type B twins (which are linked pairs) distinguishing the
prokaryote E. coli from the eukaryote S. cerevisiae. Interaction similarity is
expected due to gene duplication, and whole genome duplication paralogues in S.
cerevisiae have been reported to co-cluster into the same complexes. Indeed, we
find that these paralogous proteins are over-represented as twins compared to
pairs chosen at random. These results indicate that twinness can detect
ancestral relationships from currently available PIN data.Comment: 10 pages, 5 figures. Edited for typos, clarity, figures improved for
readabilit
Shuffled Complex-Self Adaptive Hybrid EvoLution (SC-SAHEL) optimization framework
Simplicity and flexibility of meta-heuristic optimization algorithms have attracted lots of attention in the field of optimization. Different optimization methods, however, hold algorithm-specific strengths and limitations, and selecting the best-performing algorithm for a specific problem is a tedious task. We introduce a new hybrid optimization framework, entitled Shuffled Complex-Self Adaptive Hybrid EvoLution (SC-SAHEL), which combines the strengths of different evolutionary algorithms (EAs) in a parallel computing scheme. SC-SAHEL explores performance of different EAs, such as the capability to escape local attractions, speed, convergence, etc., during population evolution as each individual EA suits differently to various response surfaces. The SC-SAHEL algorithm is benchmarked over 29 conceptual test functions, and a real-world hydropower reservoir model case study. Results show that the hybrid SC-SAHEL algorithm is rigorous and effective in finding global optimum for a majority of test cases, and that it is computationally efficient in comparison to algorithms with individual EA
VoroCrust: Voronoi Meshing Without Clipping
Polyhedral meshes are increasingly becoming an attractive option with
particular advantages over traditional meshes for certain applications. What
has been missing is a robust polyhedral meshing algorithm that can handle broad
classes of domains exhibiting arbitrarily curved boundaries and sharp features.
In addition, the power of primal-dual mesh pairs, exemplified by
Voronoi-Delaunay meshes, has been recognized as an important ingredient in
numerous formulations. The VoroCrust algorithm is the first provably-correct
algorithm for conforming polyhedral Voronoi meshing for non-convex and
non-manifold domains with guarantees on the quality of both surface and volume
elements. A robust refinement process estimates a suitable sizing field that
enables the careful placement of Voronoi seeds across the surface circumventing
the need for clipping and avoiding its many drawbacks. The algorithm has the
flexibility of filling the interior by either structured or random samples,
while preserving all sharp features in the output mesh. We demonstrate the
capabilities of the algorithm on a variety of models and compare against
state-of-the-art polyhedral meshing methods based on clipped Voronoi cells
establishing the clear advantage of VoroCrust output.Comment: 18 pages (including appendix), 18 figures. Version without compressed
images available on https://www.dropbox.com/s/qc6sot1gaujundy/VoroCrust.pdf.
Supplemental materials available on
https://www.dropbox.com/s/6p72h1e2ivw6kj3/VoroCrust_supplemental_materials.pd
The Bolocam Galactic Plane Survey. XIII. Physical Properties and Mass Functions of Dense Molecular Cloud Structures
We use the distance probability density function (DPDF) formalism of
Ellsworth-Bowers et al. (2013, 2015) to derive physical properties for the
collection of 1,710 Bolocam Galactic Plane Survey (BGPS) version 2 sources with
well-constrained distance estimates. To account for Malmquist bias, we estimate
that the present sample of BGPS sources is 90% complete above 400 and
50% complete above 70 . The mass distributions for the entire sample
and astrophysically motivated subsets are generally fitted well by a lognormal
function, with approximately power-law distributions at high mass. Power-law
behavior emerges more clearly when the sample population is narrowed in
heliocentric distance (power-law index for sources nearer
than 6.5 kpc and for objects between 2 kpc and 10 kpc).
The high-mass power-law indices are generally for
various subsamples of sources, intermediate between that of giant molecular
clouds and the stellar initial mass function. The fit to the entire sample
yields a high-mass power-law . Physical
properties of BGPS sources are consistent with large molecular cloud clumps or
small molecular clouds, but the fractal nature of the dense interstellar medium
makes difficult the mapping of observational categories to the dominant
physical processes driving the observed structure. The face-on map of the
Galactic disk's mass surface density based on BGPS dense molecular cloud
structures reveals the high-mass star-forming regions W43, W49, and W51 as
prominent mass concentrations in the first quadrant. Furthermore, we present a
0.25-kpc resolution map of the dense gas mass fraction across the Galactic disk
that peaks around 5%.Comment: Accepted for publication in ApJ; 32 pages, 21 figure
The effect of topology on the structure and free energy landscape of DNA kissing complexes
We use a recently developed coarse-grained model for DNA to study kissing
complexes formed by hybridization of complementary hairpin loops. The binding
of the loops is topologically constrained because their linking number must
remain constant. By studying systems with linking numbers -1, 0 or 1 we show
that the average number of interstrand base pairs is larger when the topology
is more favourable for the right-handed wrapping of strands around each other.
The thermodynamic stability of the kissing complex also decreases when the
linking number changes from -1 to 0 to 1. The structures of the kissing
complexes typically involve two intermolecular helices that coaxially stack
with the hairpin stems at a parallel four-way junction
Conforming restricted Delaunay mesh generation for piecewise smooth complexes
A Frontal-Delaunay refinement algorithm for mesh generation in piecewise
smooth domains is described. Built using a restricted Delaunay framework, this
new algorithm combines a number of novel features, including: (i) an
unweighted, conforming restricted Delaunay representation for domains specified
as a (non-manifold) collection of piecewise smooth surface patches and curve
segments, (ii) a protection strategy for domains containing curve segments that
subtend sharply acute angles, and (iii) a new class of off-centre refinement
rules designed to achieve high-quality point-placement along embedded curve
features. Experimental comparisons show that the new Frontal-Delaunay algorithm
outperforms a classical (statically weighted) restricted Delaunay-refinement
technique for a number of three-dimensional benchmark problems.Comment: To appear at the 25th International Meshing Roundtabl
- …