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1.
J Am Chem Soc ; 2020 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-32207939

RESUMO

Here we propose a strategy of radical oxidation reaction for the high-efficiency production of graphene oxide (GO). GO plays important roles in the sustainable development of energy and the environment, taking advantages of oxygen-containing functional groups for good dispersibility and assembly. Compared with Hummers' method, electrochemical exfoliation of graphite is considered facile and green, although the oxidation is fairly low. To synthesize GO with better crystallinity and higher oxidation degree, we present a photosynergetic electrochemical method. By using oxalate anions as the intercalation ions and co-reactant, the interfacial concentration of hydroxyl radicals generated during electrochemical exfoliation was promoted, and the oxidation degree was comparable with that of GO prepared by Hummers' method. In addition, the crystallinity was improved with fewer layers and larger size. Moreover, the aniline coassembled GO membrane was selectively permeable to water molecules by the hydrogen-bond interaction, but it was impermeable to Na+, K+, and Mg2+, due to the electrostatic interactions. Thus, it has a prospective application to water desalination and purification. This work opens a novel approach to the direct functionalization of graphene during the electroexfoliation processes and to the subsequent assembly of the functionalized graphene.

2.
Chem Commun (Camb) ; 55(23): 3379-3382, 2019 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-30820497

RESUMO

We propose programed potential modulation strategies to balance the ion intercalation/deintercalation, surface tailoring and bubbling dispersion processes in the electrochemical exfoliation of graphite, resulting in high-quality graphene with high crystallinity, low oxidation degree, uniform size distribution and few layers.

3.
ACS Appl Mater Interfaces ; 8(49): 33673-33680, 2016 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-27960387

RESUMO

A well-dispersed PtCu alloy nanoparticles (NPs) on three-dimensional nitrogen-doped graphene (PtCu/3D N-G) electrocatalyst has been successfully synthesized by a conventional hydrothermal method combined with a high-efficiency microwave-assisted polyol process. The morphology, composition, and structures are well-characterized by scanning electron microscopy, transmission electron microscopy, Raman spectroscopy, X-ray powder diffraction, and X-ray photoelectron spectroscopy. Cyclic voltammograms illustrate that the as-prepared PtCu/3D N-G electrocatalyst possesses the larger electrochemical active surface area, lower onset potential, higher current density, and better tolerance to CO poisoning than PtCu NPs on reduced graphene oxide and XC-72 carbon black in acid solution. In addition, long-time chronoamperometry reveals that the PtCu/3D N-G catalyst exhibits excellent stability even longer than 60 min toward acid methanol electrooxidation. The remarkably enhanced performance is related to the combined effects of uniformly interconnected three-dimensional porous graphene networks, nitrogen doping, modified Pt alloy NPs, and strong binding force between Pt alloy NPs and 3D N-G structures.

4.
Syst Biol ; 57(3): 335-46, 2008 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-18570030

RESUMO

As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http://loco.biosci.arizona.edu/pb), which offers a view of GenBank tailored for molecular phylogenetics. The first release of the Browser is computed from 2.6 million sequences representing the taxonomically enriched subset of GenBank sequences for eukaryotes (excluding most genome survey sequences, ESTs, and other high-throughput data). In addition to summarizing sequence diversity and species diversity across nodes in the NCBI taxonomy, it reports 87,000 potentially phylogenetically informative clusters of homologous sequences, which can be viewed or downloaded, along with provisional alignments and coarse phylogenetic trees. At each node in the NCBI hierarchy, the user can display a "data availability matrix" of all available sequences for entries in a subtaxa-by-clusters matrix. This matrix provides a guidepost for subsequent assembly of multigene data sets or supertrees. The database allows for comparison of results from previous GenBank releases, highlighting recent additions of either sequences or taxa to GenBank and letting investigators track progress on data availability worldwide. Although the reported alignments and trees are extremely approximate, the database reports several statistics correlated with alignment quality to help users choose from alternative data sources.


Assuntos
Bases de Dados de Ácidos Nucleicos , Filogenia , Software , Análise por Conglomerados , Biologia Computacional/métodos , Internet
5.
BMC Evol Biol ; 8: 90, 2008 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-18366717

RESUMO

BACKGROUND: Bioinformatic tools are needed to store and access the rapidly growing phylogenetic data. These tools should enable users to identify existing phylogenetic trees containing a specified taxon or set of taxa and to compare a specified phylogenetic hypothesis to existing phylogenetic trees. RESULTS: PhyloFinder is an intelligent search engine for phylogenetic databases that we have implemented using trees from TreeBASE. It enables taxonomic queries, in which it identifies trees in the database containing the exact name of the query taxon and/or any synonymous taxon names, and it provides spelling suggestions for the query when there is no match. Additionally, PhyloFinder can identify trees containing descendants or direct ancestors of the query taxon. PhyloFinder also performs phylogenetic queries, in which it identifies trees that contain the query tree or topologies that are similar to the query tree. CONCLUSION: PhyloFinder can enhance the utility of any tree database by providing tools for both taxonomic and phylogenetic queries as well as visualization tools that highlight the query results and provide links to NCBI and TBMap. An implementation of PhyloFinder using trees from TreeBASE is available from the web client application found in the availability and requirements section.


Assuntos
Bases de Dados Genéticas , Genômica/métodos , Armazenamento e Recuperação da Informação/métodos , Filogenia , Internet , Interface Usuário-Computador
6.
Syst Biol ; 56(4): 623-32, 2007 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-17654366

RESUMO

We describe two new methods to partition phylogenetic data sets of discrete characters based on pairwise compatibility. The partitioning methods make no assumptions regarding the phylogeny, model of evolution, or characteristics of the data. The methods first build a compatibility graph, in which each node represents a character in the data set. Edges in the compatibility graph may represent strict compatibility of characters or they may be weighted based on a fractional compatibility scoring procedure that measures how close the characters are to being compatible. Given the desired number of partitions, the partitioning methods then seek to cluster the characters with the highest average pairwise compatibility, so that characters in each cluster are more compatible with each other than they are with characters in the other cluster(s). Partitioning according to these criteria is computationally intractable (NP-hard); however, spectral methods can quickly provide high-quality solutions. We demonstrate that the spectral partitioning effectively identifies characters with different evolutionary histories in simulated data sets, and it is better at highlighting phylogenetic conflict within empirical data sets than previously used partitioning methods.


Assuntos
Simulação por Computador , Filogenia , Software
7.
Evol Bioinform Online ; 2: 347-56, 2007 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-19455229

RESUMO

The utility of the matrix representation with flipping (MRF) supertree method has been limited by the speed of its heuristic algorithms. We describe a new heuristic algorithm for MRF supertree construction that improves upon the speed of the previous heuristic by a factor of n (the number of taxa in the supertree). This new heuristic makes MRF tractable for large-scale supertree analyses and allows the first comparisons of MRF with other supertree methods using large empirical data sets. Analyses of three published supertree data sets with between 267 to 571 taxa indicate that MRF supertrees are equally or more similar to the input trees on average than matrix representation with parsimony (MRP) and modified min-cut supertrees. The results also show that large differences may exist between MRF and MRP supertrees and demonstrate that the MRF supertree method is a practical and potentially more accurate alternative to the nearly ubiquitous MRP supertree method.

8.
Artigo em Inglês | MEDLINE | ID: mdl-17048402

RESUMO

The input to a supertree problem is a collection of phylogenetic trees that intersect pairwise in their leaf sets; the goal is to construct a single tree that retains as much as possible of the information in the input. This task is complicated by inconsistencies due to errors. We consider the case where the input trees are rooted and are represented by the clusters they exhibit. The problem is to find the minimum number of flips needed to resolve all inconsistencies, where each flip moves a taxon into or out of a cluster. We prove that the minimum-flip problem is NP-complete, but show that it is fixed-parameter tractable and give approximation algorithms for special cases.


Assuntos
Algoritmos , Biologia Computacional/métodos , Filogenia , Evolução Molecular , Modelos Genéticos
9.
Syst Biol ; 53(2): 299-308, 2004 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-15205054

RESUMO

Supertree methods are used to assemble separate phylogenetic trees with shared taxa into larger trees (supertrees) in an effort to construct more comprehensive phylogenetic hypotheses. In spite of much recent interest in supertrees, there are still few methods for supertree construction. The flip supertree problem is an error correction approach that seeks to find a minimum number of changes (flips) to the matrix representation of the set of input trees to resolve their incompatibilities. A previous flip supertree algorithm was limited to finding exact solutions and was only feasible for small input trees. We developed a heuristic algorithm for the flip supertree problem suitable for much larger input trees. We used a series of 48- and 96-taxon simulations to compare supertrees constructed with the flip supertree heuristic algorithm with supertrees constructed using other approaches, including MinCut (MC), modified MC (MMC), and matrix representation with parsimony (MRP). Flip supertrees are generally far more accurate than supertrees constructed using MC or MMC algorithms and are at least as accurate as supertrees built with MRP. The flip supertree method is therefore a viable alternative to other supertree methods when the number of taxa is large.


Assuntos
Algoritmos , Classificação/métodos , Filogenia , Simulação por Computador
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