599 research outputs found
Self Consistent Expansion for the Molecular Beam Epitaxy Equation
Motivated by a controversy over the correct results derived from the dynamic
renormalization group (DRG) analysis of the non linear molecular beam epitaxy
(MBE) equation, a self-consistent expansion (SCE) for the non linear MBE theory
is considered. The scaling exponents are obtained for spatially correlated
noise of the general form . I find a lower critical dimension , above, which the linear MBE solution appears. Below the
lower critical dimension a r-dependent strong-coupling solution is found. These
results help to resolve the controversy over the correct exponents that
describe non linear MBE, using a reliable method that proved itself in the past
by predicting reasonable results for the Kardar-Parisi-Zhang (KPZ) system,
where DRG failed to do so.Comment: 16 page
Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community
Background: Caenorhabditis elegans gene-based phenotype information dates back to the 1970’s, beginning with
Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in
order to understand nervous system function. Since then C. elegans has become an important genetic model
system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis.
Because of the growth of C. elegans as a genetically tractable model organism and the development of large-scale
analyses, there has been a significant increase of phenotype data that needs to be managed and made accessible
to the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from
diverse sources, permit integration with other data types and render the data in a computable form.
Results: We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize
phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO). The WPO is currently
comprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated
with greater than 18,000 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans biology,
rather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the
value of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes
to non-nematode biologists. We are actively developing the WPO to continue to fulfill the evolving needs of the
scientific community and hope to engage researchers in this crucial endeavor.
Conclusions: We provide a phenotype ontology (WPO) that will help to facilitate data retrieval, and cross-species
comparisons within the nematode community. In the larger scientific community, the WPO will permit data
integration, and interoperability across the different Model Organism Databases (MODs) and other biological
databases. This standardized phenotype ontology will therefore allow for more complex data queries and enhance
bioinformatic analyses
Diffusive Capture Process on Complex Networks
We study the dynamical properties of a diffusing lamb captured by a diffusing
lion on the complex networks with various sizes of . We find that the life
time and the survival probability becomes finite on scale-free networks with degree exponent
. However, for has a long-living tail on
tree-structured scale-free networks and decays exponentially on looped
scale-free networks. It suggests that the second moment of degree distribution
kn(k)n(k)\sim k^{-\sigma}\gamma<3n(k)k\approx k_{max}n(k)n(k)\sim k^2P(k)N_{tot}, which
causes the dependent behavior of and $.Comment: 9 pages, 6 figure
Self-similar disk packings as model spatial scale-free networks
The network of contacts in space-filling disk packings, such as the
Apollonian packing, are examined. These networks provide an interesting example
of spatial scale-free networks, where the topology reflects the broad
distribution of disk areas. A wide variety of topological and spatial
properties of these systems are characterized. Their potential as models for
networks of connected minima on energy landscapes is discussed.Comment: 13 pages, 12 figures; some bugs fixed and further discussion of
higher-dimensional packing
WormBase 2007
WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from the initial ACeDB database of C. elegans genetic and sequence information, WormBase now includes the genomic, anatomical and functional information about C. elegans, other Caenorhabditis species and other nematodes. As such, it is a crucial resource not only for C. elegans biologists but the larger biomedical and bioinformatics communities. Coverage of core areas of C. elegans biology will allow the biomedical community to make full use of the results of intensive molecular genetic analysis and functional genomic studies of this organism. Improved search and display tools, wider cross-species comparisons and extended ontologies are some of the features that will help scientists extend their research and take advantage of other nematode species genome sequences
An air-stable DPP-thieno-TTF copolymer for single-material solar cell devices and field effect transistors
Following an approach developed in our group to incorporate tetrathiafulvalene (TTF) units into conjugated polymeric systems, we have studied a low band gap polymer incorporating TTF as a donor component. This polymer is based on a fused thieno-TTF unit that enables the direct incorporation of the TTF unit into the polymer, and a second comonomer based on the diketopyrrolopyrrole (DPP) molecule. These units represent a donor–acceptor copolymer system, p(DPP-TTF), showing strong absorption in the UV–visible region of the spectrum. An optimized p(DPP-TTF) polymer organic field effect transistor and a single material organic solar cell device showed excellent performance with a hole mobility of up to 5.3 × 10–2 cm2/(V s) and a power conversion efficiency (PCE) of 0.3%, respectively. Bulk heterojunction organic photovoltaic devices of p(DPP-TTF) blended with phenyl-C71-butyric acid methyl ester (PC71BM) exhibited a PCE of 1.8%
Toward an interactive article: integrating journals and biological databases.
BACKGROUND: Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. RESULTS: We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases. CONCLUSIONS: Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are
Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks
The evolution and adaptation of molecular populations is constrained by the diversity accessible through mutational processes. RNA is a paradigmatic example of biopolymer where genotype (sequence) and phenotype (approximated by the secondary structure fold) are identified in a single molecule. The extreme redundancy of the genotype-phenotype map leads to large ensembles of RNA sequences that fold into the same secondary structure and can be connected through single-point mutations. These ensembles define neutral networks of phenotypes in sequence space. Here we analyze the topological properties of neutral networks formed by 12-nucleotides RNA sequences, obtained through the exhaustive folding of sequence space. A total of 412 sequences fragments into 645 subnetworks that correspond to 57 different secondary structures. The topological analysis reveals that each subnetwork is far from being random: it has a degree distribution with a well-defined average and a small dispersion, a high clustering coefficient, and an average shortest path between nodes close to its minimum possible value, i.e. the Hamming distance between sequences. RNA neutral networks are assortative due to the correlation in the composition of neighboring sequences, a feature that together with the symmetries inherent to the folding process explains the existence of communities. Several topological relationships can be analytically derived attending to structural restrictions and generic properties of the folding process. The average degree of these phenotypic networks grows logarithmically with their size, such that abundant phenotypes have the additional advantage of being more robust to mutations. This property prevents fragmentation of neutral networks and thus enhances the navigability of sequence space. In summary, RNA neutral networks show unique topological properties, unknown to other networks previously described
Statistical mechanics of complex networks
Complex networks describe a wide range of systems in nature and society, much
quoted examples including the cell, a network of chemicals linked by chemical
reactions, or the Internet, a network of routers and computers connected by
physical links. While traditionally these systems were modeled as random
graphs, it is increasingly recognized that the topology and evolution of real
networks is governed by robust organizing principles. Here we review the recent
advances in the field of complex networks, focusing on the statistical
mechanics of network topology and dynamics. After reviewing the empirical data
that motivated the recent interest in networks, we discuss the main models and
analytical tools, covering random graphs, small-world and scale-free networks,
as well as the interplay between topology and the network's robustness against
failures and attacks.Comment: 54 pages, submitted to Reviews of Modern Physic
Search for decays to invisible final states at Belle
We report the result from the first search for decays to invisible
final states. The analysis is performed on a data sample of 924
collected at and near the and resonances with the
Belle detector at the KEKB asymmetric-energy collider. The
absolute branching fraction is determined using an inclusive sample,
obtained by fully reconstructing the rest of the particle system including the
other charmed particle. No significant signal yield is observed and an upper
limit of is set on the branching fraction of to
invisible final states at 90\% confidence level.Comment: 17 pages, 4 figures, submitted to PRD(RC
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