13,835 research outputs found
DNA computing by blocking
AbstractWe present a method for molecular computing which relies on blocking (inactivating) this part of the total library of molecules that does not contribute to (finding) a solution—this happens essentially in one biostep (after the input has been read). The method is explained by presenting a DNA based algorithm for solving (albeit in the theoretical sense only!) the satisfiability problem
Designable electron transport features in one-dimensional arrays of metallic nanoparticles: Monte Carlo study of the relation between shape and transport
We study the current and shot noise in a linear array of metallic
nanoparticles taking explicitly into consideration their discrete electronic
spectra. Phonon assisted tunneling and dissipative effects on single
nanoparticles are incorporated as well. The capacitance matrix which determines
the classical Coulomb interaction within the capacitance model is calculated
numerically from a realistic geometry. A Monte Carlo algorithm which
self-adapts to the size of the system allows us to simulate the single-electron
transport properties within a semiclassical framework. We present several
effects that are related to the geometry and the one-electron level spacing
like e.g. a negative differential conductance (NDC) effect. Consequently these
effects are designable by the choice of the size and arrangement of the
nanoparticles.Comment: 13 pages, 12 figure
What goes in, must come out:combining scat-based molecular diet analysis and quantification of ingested microplastics in a marine top predator
Context: Microplastics (plastic particles <5 mm in size) are highly available for ingestion by a wide range of organisms, either through direct consumption or indirectly, via trophic transfer, from prey to predator. The latter is a poorly understood, but potentially major, route of microplastic ingestion for marine top predators.Approach: We developed a novel and effective methodology pipeline to investigate dietary exposure of wild top predators (grey seals; Halichoerus grypus) to microplastics, by combining scat-based molecular techniques with a microplastic isolation method. We employed DNA metabarcoding, a rapid method of biodiversity assessment, to garner detailed information on prey composition from scats, and investigated the potential relationship between diet and microplastic burden.Results: Outcomes of the method development process and results of both diet composition from metabarcoding analysis and detection of microplastics are presented. Importantly, the pipeline performed well and initial results suggest the frequency of microplastics detected in seal scats may be related to the type of prey consumed. Conclusions: Our non-invasive, data rich approach maximises time and resource-efficiency, while minimising costs and sample volumes required for analysis. This pipeline could be used to underpin a much-needed increase in understanding of the relationship between diet composition and rates of microplastic ingestion in high trophic-level species.<br/
Noncooperative algorithms in self-assembly
We show the first non-trivial positive algorithmic results (i.e. programs
whose output is larger than their size), in a model of self-assembly that has
so far resisted many attempts of formal analysis or programming: the planar
non-cooperative variant of Winfree's abstract Tile Assembly Model.
This model has been the center of several open problems and conjectures in
the last fifteen years, and the first fully general results on its
computational power were only proven recently (SODA 2014). These results, as
well as ours, exemplify the intricate connections between computation and
geometry that can occur in self-assembly.
In this model, tiles can stick to an existing assembly as soon as one of
their sides matches the existing assembly. This feature contrasts with the
general cooperative model, where it can be required that tiles match on
\emph{several} of their sides in order to bind.
In order to describe our algorithms, we also introduce a generalization of
regular expressions called Baggins expressions. Finally, we compare this model
to other automata-theoretic models.Comment: A few bug fixes and typo correction
Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
Gaining a genomic perspective on phylogeny requires the collection of data
from many putatively independent loci collected across the genome. Among
insects, an increasingly common approach to collecting this class of data
involves transcriptome sequencing, because few insects have high-quality genome
sequences available; assembling new genomes remains a limiting factor; the
transcribed portion of the genome is a reasonable, reduced subset of the genome
to target; and the data collected from transcribed portions of the genome are
similar in composition to the types of data with which biologists have
traditionally worked (e.g., exons). However, molecular techniques requiring RNA
as a template are limited to using very high quality source materials, which
are often unavailable from a large proportion of biologically important insect
samples. Recent research suggests that DNA-based target enrichment of conserved
genomic elements offers another path to collecting phylogenomic data across
insect taxa, provided that conserved elements are present in and can be
collected from insect genomes. Here, we identify a large set (n1510) of
ultraconserved elements (UCE) shared among the insect order Hymenoptera. We use
in silico analyses to show that these loci accurately reconstruct relationships
among genome-enabled Hymenoptera, and we design a set of baits for enriching
these loci that researchers can use with DNA templates extracted from a variety
of sources. We use our UCE bait set to enrich an average of 721 UCE loci from
30 hymenopteran taxa, and we use these UCE loci to reconstruct phylogenetic
relationships spanning very old (220 MYA) to very young (1 MYA)
divergences among hymenopteran lineages. In contrast to a recent study
addressing hymenopteran phylogeny using transcriptome data, we found ants to be
sister to all remaining aculeate lineages with complete support
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