Streamline topology and dilute particle dynamics in a Karman vortex street flow

Three types of streamline topology in a Karman vortex street flow are shown under the variation of spatial parameters. For the motion of dilute particles in the Karman vortex street flow, there exist a route of bifurcation to a chaotic orbit and more attractors in a bifurcation diagram for the proportion of particle density to fluid density. Along with the increase of spatial parameters in the flow field, the bifurcation process is suspended, as well as more and more attractors emerge. In the motion of dilute particles, a drag term and gravity term dominate and result in the bifurcation phenomenon.

Topology of toroidal helical fields in non-circular cross-sectional tokamaks

The ordinary differential magnetic field line equations are solved numerically; the tokamak magnetic structure is studied on Hefei Tokamak-7 Upgrade (HT-7U) when the equilibrium field with a monotonic q-profile is perturbed by a helical magnetic field. We find that a single mode (m, n) helical perturbation can cause the formation of islands on rational surfaces with q = m/n and q = (m +/- 1, +/- 2, +/- 3,...)/n due to the toroidicity and plasma shape (i.e. elongation and triangularity), while there are many undestroyed magnetic surfaces called Kolmogorov-Arnold-Moser (KAM) barriers on irrational surfaces. The islands on the same rational surface do not have the same size. When the ratio between the perturbing magnetic field B-r(r) and the toroidal magnetic field amplitude B(phi)0 is large enough, the magnetic island chains on different rational surfaces will overlap and chaotic orbits appear in the overlapping area, and the magnetic field becomes stochastic. It is remarkable that the stochastic layer appears first in the plasma edge region.

The further understanding of chain topology effect on the properties of single polymer in good solvent: Special behaviors of single tadpole chain

Chain topology strongly affects the static and dynamic properties of polymer melts and polymers in dilute solution. For different chain architectures, such as ring and linear polymers, the molecular size and the diffusion behavior are different. To further understand the chain topology effect on the static and dynamic properties of polymers, we focus on the tadpole polymer which consists of a cyclic chain attached with one or more linear tails. It is found that both the number and the length of linear tails play important roles on the properties of the tadpole polymers in dilute solution. For the tadpole polymers with fixed linear tail length and number, with increasing the degree of polymerization of tadpole polymers, a transition from linear-like to ring-like behavior is observed for both the static and dynamic properties.

Influence of molecular topology on the static and dynamic properties of single polymer chain in solution

The influence of molecular topology on the structural and dynamic properties of polymer chain in solution with ring structure, three-arm branched structure, and linear structure are studied by molecular dynamics simulation. At the same degree of polymerization (N), the ring-shaped chain possesses the smallest size and largest diffusion coefficient. With increasing N, the difference of the radii of gyration between the three types of polymer chains increases, whereas the difference of the diffusion coefficients among them decreases. However, the influence of the molecular topology on the static and the dynamic scaling exponents is small. The static scaling exponents decrease slightly, and the dynamic scaling exponents increase slightly, when the topology of the polymer chain is changed from linear to ring-shaped or three-arm branched architecture. The dynamics of these three types of polymer chain in solution is Zimm-like according to the dynamic scaling exponents and the dynamic structure factors.

STRUCTURE-PROPERTY RELATIONSHIP BETWEEN HALF-WAVE POTENTIALS OF ORGANIC-COMPOUNDS AND THEIR TOPOLOGY

A significant correlation was found between half-wave potentials of organic compounds and their topological indices, A(x1), A(x2), and A(x3). The simplicity of calculation of the index from the connectivity in the molecular skeleton, together with the significant correlation, indicates its practical value. Good results have been obtained by using them to predict the half-wave potentials of some organic compounds.

Unprecedented 5,5-connected (4(7)center dot 6(3)) (4(8)center dot 6(2)) structural topology: A lead biphosphonate with double layered structure

A new lead(II) phosphonate, Pb[(PO3)(2)C(OH)CH3]center dot H2O (1) was hydrothermally synthesized and characterized by IR, elemental analysis, UV, TGA, SEM, and single crystal X-ray diffraction analysis. X-ray crystallographic study showed that complex 1 has a two-dimensional double layered hybrid structure containing interconnected 4- and 12-membered rings and shows an unusual (5,5)-connected (4(7) . 6(3)) (4(8) .6(2)) topology. (C) 2008 Elsevier B.V. All rights reserved.

Pattern Recognition With Weighted Complex Networks

In this paper we introduce a weighted complex networks model to investigate and recognize structures of patterns. The regular treating in pattern recognition models is to describe each pattern as a high-dimensional vector which however is insufficient to express the structural information. Thus, a number of methods are developed to extract the structural information, such as different feature extraction algorithms used in pre-processing steps, or the local receptive fields in convolutional networks. In our model, each pattern is attributed to a weighted complex network, whose topology represents the structure of that pattern. Based upon the training samples, we get several prototypal complex networks which could stand for the general structural characteristics of patterns in different categories. We use these prototypal networks to recognize the unknown patterns. It is an attempt to use complex networks in pattern recognition, and our result shows the potential for real-world pattern recognition. A spatial parameter is introduced to get the optimal recognition accuracy, and it remains constant insensitive to the amount of training samples. We have discussed the interesting properties of the prototypal networks. An approximate linear relation is found between the strength and color of vertexes, in which we could compare the structural difference between each category. We have visualized these prototypal networks to show that their topology indeed represents the common characteristics of patterns. We have also shown that the asymmetric strength distribution in these prototypal networks brings high robustness for recognition. Our study may cast a light on understanding the mechanism of the biologic neuronal systems in object recognition as well.

Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree

We have made a set of chromosome-specific painting probes for the American mink by degenerate oligonucleotide primed-PCR (DOP-PCR) amplification of flow-sorted chromosomes. The painting probes were used to delimit homologous chromosomal segments among human, red fox, dog, cat and eight species of the family Mustelidae, including the European mink, steppe and forest polecats, least weasel, mountain weasel, Japanese sable, striped polecat, and badger. Based on the results of chromosome painting and G-banding, comparative maps between these species have been established. The integrated map demonstrates a high level of karyotype conservation among mustelid species. Comparative analysis of the conserved chromosomal segments among mustelids and outgroup species revealed 18 putative ancestral autosomal segments that probably represent the ancestral chromosomes, or chromosome arms, in the karyotype of the most recent ancestor of the family Mustelidae. The proposed 2n = 38 ancestral Mustelidae karyotype appears to have been retained in some modern mustelids, e.g., Martes, Lutra, ktonyx, and Vormela. The derivation of the mustelid karyotypes from the putative ancestral state resulted from centric fusions, fissions, the addition of heterochromatic arms, and occasional pericentric inversions. Our results confirm many of the evolutionary conclusions suggested by other data and strengthen the topology of the carnivore phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. Copyright (C) 2002 S. KargerAG, Basel.

Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples

As an endangered animal group, musk deer (genus Moschus) are not only a great concern of wildlife conservation, but also of special interest to evolutionary studies due to long-standing arguments on the taxonomic and phylogenetic associations in this group. Using museum samples, we sequenced complete mitochondrial cytochrome b genes (1140 bp) of all suggested species of musk deer in order to reconstruct their phylogenetic history through molecular information. Our results showed that the cytochrome b gene tree is rather robust and concurred for all the algorithms employed (parsimony, maximum likelihood, and distance methods). Further, the relative rate test indicated a constant sequence substitution rate among all the species, permitting the dating of divergence events by molecular clock. According to the molecular topology, M. moschiferus branched off the earliest from a common ancestor of musk deer (about 700,000 years ago); then followed the bifurcation forming the M. berezouskii lineage and the lineage clustering M. fuscus, M. chrysogaster, and M. leucogaster (around 370,000 years before present), interestingly the most recent speciation event in musk deer happened rather recently (140,000 years ago), which might have resulted from the diversified habitats and geographic barriers in southwest China caused by gigantic movements of the Qinghai-Tibetan Plateau in history. Combining the data of current distributions, fossil records, and molecular data of this study, we suggest that the historical dispersion of musk deer might be from north to south in China. Additionally, in our further analyses involving other pecora species, musk deer was strongly supported as a monophyletic group and a valid family in Artiodactyla, closely related to Cervidae. (C) 1999 Academic Press.

Phylogeny of Muntiacus (Cervidae) based on mitochondrial DNA restriction maps

Mitochondrial DNA restriction maps for 12 restriction enzymes of four species of muntjacs-Indian muntjac (M. muntjak), Gongshan muntjac (M. gongshanensis), black muntjac (M. crinifrons), and Chinese muntjac (M. reevesi)-were compared to estimate the phylogenetic relationships among them. Phylogenetic trees were constructed by both distance and parsimony methods. The two resulting trees share a similar topology, which indicates that the black muntjac and the Gongshan muntjac are closely related, followed by the Chinese muntjac; the Indian muntjac is the sister taxon to all the other muntjacs.

Molecular systematics of medusae in the genus Craspedacusta (Cnidaria: Hydrozoa: Limnomedusae) in China with the reference to the identity of species

The objective of this study was to illustrate the phylogenetic relationship of the species in the genus Craspedacusta in China. The medusae samples were collected at 28 localities in China representing seven described species with their entire ITS region (the contiguous sequences of ITS-1, 5.8S and ITS-2 rDNA) rDNA sequences cloned. Among the 28 samples, the range of sequence variation in the complete ITS and 5.8S region was between 0 and 36.2%. Three main clades were revealed by both maximum likelihood and neighbour-joining trees, with sequence difference of 0-0.9, 0-3.7 and 0.1-1.5% in the three clades. The nesting of C. xinyangensis representatives within C. sowerbii, C. brevinema within C. sinensis and C. sichuanensis within C. kiatingi is strongly supported, with interspecific sequence divergence of 0-0.9, 0.1-1.4 and 0.0-0.4%, respectively. Thus, it is suggested that C. xinyangensis should be the synonym of C. sowerbii, C. sichuanensis the synonym of C. kiatingi and C. brevinema the synonym of C. sinensis. However, the taxonomic status of C. ziguiensis is still uncertain. According to the tree topology, C. kiatingi was closer to C. sowerbii than to C. sinensis. Craspedacusta sinensis was the most genetically distinct from distance matrix values, and located at the base of the phylogenetic trees, so it can be speculated that the C. sinensis may be the ancestral form in the genus Craspedacusta.

Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys

The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub-species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree-building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub-species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8.89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4.78 mya from the Chinese group. The northern-southern clades of S. nigripinnis began to diverge c. 2.12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0.34 mya. (C) 2008 The Authors Journal compilation (C) 2008 The Fisheries Society of the British Isles.

The c-myc coding DNA sequences of cyprinids (Teleostei : Cypriniformes): Implications for phylogeny

The family Cyprinidae is one of the largest fish families in the world, which is widely distributed in East Asian, with obvious difference in characteristic size among species. The phylogenetic analysis of cyprinid taxa based on the functionally important genes can help to understand the speciation and functional divergench of the Cyprinidae. The c-myc gene is an important gene regulating individual growth. In the present study, the sequence variations of the cyprinid c-myc gene and their phylogenetic significance were analyzed. The 41 complete sequences of the c-myc gene were obtained from cyprinids and outgroups through PCR amplification and clone. The coding DNA sequences of the c-myc gene were used to infer molecular phylogenetic relationships within the Cyprinidae. Myxocyprinus asiaticus (Catostomidae), Misgurnus anguillicaudatus (Cobitidae) and Hemimyzon sinensis (Homalopteridae) were assigned to the outgroup taxa. Phylogenetic analyses using maximum parsimony (MP), maximum likelihood (ML), and Bayesian retrieved similar topology. Within the Cyprinidae, Leuciscini and Barbini formed the monophyletic lineage respectively with high nodal supports. Leuciscini comprises Xeno-cyprinae, Cultrinae, East Asian species of Leuciscinae and Danioninae, Gobioninae and Acheilognathinae, and Barbini contains Schizothoracinae, Barbinae, Cyprininae and Labeoninae. Danio rerio, D. myersi and Rasbora trilineata were supposed to separate from Leuciscinae and Barbini and to form another lineage, The positions of some Danioninae species were still unresolved. Analyses of both amino acid variation with parsimony information and two high variation regions indicated that there is no correlation between variations of single amino acid or high variation regions and characteristic size of cyprinids. In,addition, the species with smaller size were usually found to be basal within clades in the tree, which might be the results of the adaptation to the primitive ecology and survival pressure.

Phylogeny of diplozoids in five genera of the subfamily diplozoinae palombi, 1949 as inferred from ITS-2 rDNA sequences

The phylogenetic relationship of 5 genera, i.e. Diplozoon Nordmann, 1832, Paradiplozoon Achmerov, 1974, Inustiatus Khotenovsky, 1978, Sindiplozoon Khotenovsky, 1981, and Eudiplozoon Khotenovsky, 1985 in the subfamily Diplozoinae Palombi, 1949 (Monogenea, Polyopisthocotylea) was inferred from rDNA ITS-2 region using neighbour-joining (NJ), maximum likelihood (ML) and Bayesian methods. The phylogenetic trees produced by using NJ, ML and Bayesian methods exhibit essentially the same topology. Surprisingly, freshwater species of Paradiplozoon from Europe clustered together with species of Diplozoon, but separated from Chinese Paradiplozoon species. The results of molecular phylogeny and lower level of divergence (4(.)1-15(.)7%) in ITS-2 rDNA among Paradiplozoon from Europe and Diplozoon and, on the other hand, high level of divergence (45(.)3-53(.)7%) among Paradiplozoon species from Europe and China might indicate the non-monophyletic origin of the genus Paradiplozoon. Also, the generic status of European Paradiplozoon needs to be revised. The species of Paradiplozoon in China is a basal group in Diplozoinae as revealed by NJ and Bayesian methods, and Sindiplozoon appears to be closely related to European Paradiplozoon and Diplozoon. with their relationship to Eudiplozoon and Inustiatus being unresolved.