170 research outputs found
Stone-Wales Transformation Paths in Fullerene C60
The mechanisms of formation of a metastable defect isomer of fullerene C60
due to the Stone-Wales transformation are theoretically studied. It is
demonstrated that the paths of the "dynamic" Stone-Wales transformation at a
high sufficient for overcoming potential barriers) temperature can differ from
the two "adiabatic" transformation paths discussed in the literature. This
behavior is due to the presence of a great near-flat segment of the
potential-energy surface in the neighborhood of metastable states. Besides, the
sequence of rupture and formation of interatomic bonds is other than that in
the case of the adiabatictransformation.Comment: 10 pages, 6 figure
Energy Landscape and Global Optimization for a Frustrated Model Protein
The three-color (BLN) 69-residue model protein was designed to exhibit frustrated folding. We investigate the energy landscape of this protein using disconnectivity graphs and compare it to a Go model, which is designed to reduce the frustration by removing all non-native attractive interactions. Finding the global minimum on a frustrated energy landscape is a good test of global optimization techniques, and we present calculations evaluating the performance of basin-hopping and genetic algorithms for this system.Comparisons are made with the widely studied 46-residue BLN protein.We show that the energy landscape of the 69-residue BLN protein contains several deep funnels, each of which corresponds to a different β-barrel structure
Use of a polyphasic approach including MALDI-TOF MS for identification of Aspergillus section Flavi strains isolated from food commodities in Brazil
Brazil is one the largest producers and exporters of food commodities in the world. The evaluation of fungi capable of spoilage and the production mycotoxins in these commodities is an important issue that can be of help in bioeconomic development. The present work aimed to identify fungi of the genus Aspergillus section Flavi isolated from different food commodities in Brazil. Thirty-five fungal isolates belonging to the section Flavi were identified and characterised. Different classic phenotypic and genotypic methodologies were used, as well as a novel approach based on proteomic profiles produced by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Type or reference strains for each taxonomic group were included in this study. Three isolates that presented discordant identification patterns were further analysed using the internal transcribed spacer (ITS) region and calmodulin gene sequences. The data obtained from the phenotypic and spectral analyses divide the isolates into three groups, corresponding to taxa closely related to Aspergillus flavus, Aspergillus parasiticus, and Aspergillus tamarii. Final polyphasic fungal identification was achieved by joining data from molecular analyses, classical morphology, and biochemical and proteomic profiles generated by MALDI-TOF MS.Acknowledgments are due to FAPEMIG -
Fundacao de Amparo a Pesquisa do Estado de Minas Gerais (Brazil)
for financial support. F. C. da Silva extends thanks to CAPES -
Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (Brazil)
for the PhD grant. C. Santos and N. Lima thank CAPES for the financial
support as international visiting professors in the Post-Graduate Programme
in Agricultural Microbiology, Federal University of Lavras,
Lavras (MG), Brazil
What can comparative genomics tell us about species concepts in the genus Aspergillus?
Understanding the nature of species” boundaries is a fundamental
question in evolutionary biology. The availability of genomes from several
species of the genus Aspergillus allows us for the first time to
examine the demarcation of fungal species at the whole-genome level. Here, we
examine four case studies, two of which involve intraspecific comparisons,
whereas the other two deal with interspecific genomic comparisons between
closely related species. These four comparisons reveal significant variation
in the nature of species boundaries across Aspergillus. For example,
comparisons between A. fumigatus and Neosartorya fischeri
(the teleomorph of A. fischerianus) and between A. oryzae
and A. flavus suggest that measures of sequence similarity and
species-specific genes are significantly higher for the A. fumigatus
- N. fischeri pair. Importantly, the values obtained from the
comparison between A. oryzae and A. flavus are remarkably
similar to those obtained from an intra-specific comparison of A.
fumigatus strains, giving support to the proposal that A. oryzae
represents a distinct ecotype of A. flavus and not a distinct
species. We argue that genomic data can aid Aspergillus taxonomy by
serving as a source of novel and unprecedented amounts of comparative data, as
a resource for the development of additional diagnostic tools, and finally as
a knowledge database about the biological differences between strains and
species
Quasi-continuous Interpolation Scheme for Pathways between Distant Configurations
A quasi-continuous interpolation (QCI) scheme is introduced for characterizing physically realistic initial pathways from which to initiate transition state searches and construct kinetic transition networks. Applications are presented for peptides, proteins, and a morphological transformation in an atomic cluster. The first step in each case involves end point alignment, and we describe the use of a shortest augmenting path algorithm for optimizing permutational isomers. The QCI procedure then employs an interpolating potential, which preserves the covalent bonding framework for the biomolecules and includes repulsive terms between unconstrained atoms. This potential is used to identify an interpolating path by minimizing contributions from a connected set of images, including terms corresponding to minima in the interatomic distances between them. This procedure detects unphysical geometries in the line segments between images. The most difficult cases, where linear interpolation would involve chain crossings, are treated by growing the structure an atom at a time using the interpolating potential. To test the QCI procedure, we carry through a series of benchmark calculations where the initial interpolation is coupled to explicit transition state searches to produce complete pathways between specified local minima.This work was supported by the Engineering and Physical Sciences Research Council [grant number EP/H042660/1]This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in the Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review. To access the final edited and published work see http://dx.doi.org/10.1021/ct300483
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