1,774 research outputs found
Thiol density dependent classical potential for methyl-thiol on a Au(111) surface
A new classical potential for methyl-thiol on a Au(111) surface has been
developed using density functional theory electronic structure calculations.
Energy surfaces between methyl-thiol and a gold surface were investigated in
terms of symmetry sites and thiol density. Geometrical optimization was
employed over all the configurations while minimum energy and thiol height were
determined. Finally, a new interatomic potential has been generated as a
function of thiol density, and applications to coarse-grained simulations are
presented
Parallel TREE code for two-component ultracold plasma analysis
The TREE method has been widely used for long-range interaction {\it N}-body
problems. We have developed a parallel TREE code for two-component classical
plasmas with open boundary conditions and highly non-uniform charge
distributions. The program efficiently handles millions of particles evolved
over long relaxation times requiring millions of time steps. Appropriate domain
decomposition and dynamic data management were employed, and large-scale
parallel processing was achieved using an intermediate level of granularity of
domain decomposition and ghost TREE communication. Even though the
computational load is not fully distributed in fine grains, high parallel
efficiency was achieved for ultracold plasma systems of charged particles. As
an application, we performed simulations of an ultracold neutral plasma with a
half million particles and a half million time steps. For the long temporal
trajectories of relaxation between heavy ions and light electrons, large
configurations of ultracold plasmas can now be investigated, which was not
possible in past studies
Molecular Species Identification with Rich Floristic Sampling: DNA Barcoding the Pteridophyte Flora of Japan
BACKGROUND: DNA barcoding is expected to be an effective identification tool for organisms with heteromorphic generations such as pteridophytes, which possess a morphologically simple gametophyte generation. Although a reference data set including complete coverage of the target local flora/fauna is necessary for accurate identification, DNA barcode studies including such rich taxonomic sampling on a countrywide scale are lacking. METHODOLOGY/PRINCIPAL FINDINGS: The Japanese pteridophyte flora (733 taxa including subspecies and varieties) was used to test the utility of two plastid DNA barcode regions (rbcL and trnH-psbA) with the intention of developing an identification system for native gametophytes. DNA sequences were obtained from each of 689 (94.0%) taxa for rbcL and 617 (84.2%) taxa for trnH-psbA. Mean interspecific divergence values across all taxon pairs (K2P genetic distances) did not reveal a significant difference in rate between trnH-psbA and rbcL, but mean K2P distances of each genus showed significant heterogeneity according to systematic position. The minimum fail rate of taxon discrimination in an identification test using BLAST (12.52%) was obtained when rbcL and trnH-psbA were combined, and became lower in datasets excluding infraspecific taxa or apogamous taxa, or including sexual diploids only. CONCLUSIONS/SIGNIFICANCE: This study demonstrates the overall effectiveness of DNA barcodes for species identification in the Japanese pteridophyte flora. Although this flora is characterized by a high occurrence of apogamous taxa that pose a serious challenge to identification using DNA barcodes, such taxa are limited to a small number of genera, and only minimally detract from the overall success rate. In the case that a query sequence is matched to a known apogamous genus, routine species identification may not be possible. Otherwise, DNA barcoding is a practical tool for identification of most Japanese pteridophytes, and is especially anticipated to be helpful for identification of non-hybridizing gametophytes
- …