Topologically invariant reaction coordinates for simulating multistate chemical reactions.

Evaluating free energy profiles of chemical reactions in complex environments such as solvents and enzymes requires extensive sampling, which is usually performed by potential of mean force (PMF) techniques. The reliability of the sampling depends not only on the applied PMF method but also the reaction coordinate space within the dynamics is biased. In contrast to simple geometrical collective variables that depend only on the positions of the atomic coordinates of the reactants, the E(gap) reaction coordinate (the energy difference obtained by evaluating a suitable force field using reactant and product state topologies) has the unique property that it is able to take environmental effects into account leading to better convergence, a more faithful description of the transition state ensemble and therefore more accurate free energy profiles. However, E(gap) requires predefined topologies and is therefore inapplicable for multistate reactions, in which the barrier between the chemically equivalent topologies is comparable to the reaction activation barrier, because undesired "side reactions" occur. In this article, we introduce a new energy-based collective variable by generalizing the E(gap) reaction coordinate such that it becomes invariant to equivalent topologies and show that it yields more well behaved free energy profiles than simpler geometrical reaction coordinates.

FPGA, physics-based modeling of IGBT and pin diode for hardware co-simulation of complex power electronic converters and systems

This paper presents the steps and the challenges for implementing analytical, physics-based models for the insulated gate bipolar transistor (IGBT) and the PIN diode in hardware and more specifically in field programmable gate arrays (FPGAs). The models can be utilised in hardware co-simulation of complex power electronic converters and entire power systems in order to reduce the simulation time without compromising the accuracy of results. Such a co-simulation allows reliable prediction of the system's performance as well as accurate investigation of the power devices' behaviour during operation. Ultimately, this will allow application-specific optimisation of the devices' structure, circuit topologies as well as enhancement of the control and/or protection schemes.

母鸡输卵管子宫部初级感觉神经元的CB-HRP法定位研究

应用CB-HRP溶液注入母鸡输卵管子宫部浆膜下,四甲基联苯胺(TMB)组织化学呈色,以探察母鸡输卵管子宫部初级感觉神经元的定位。结果表明:母鸡输卵管子宫部的初级感觉神经元位于双侧T1-LS13脊神经节、颈静脉神经节和结状神经节。标记细胞数分布不均,在体左侧多于体右侧,在脊神经节多于颈静脉神经节和结状神经节。在脊神经节内标记细胞有T5-LS1和LS8-LS11前后两个相对集中区,峰值分别在T7和LS11。说明尽管母鸡输卵管子宫部是单侧发育成熟脏器,但其感觉沿双侧脊神经和迷走神经传入中枢,以体左侧传入为主;且

Stiffness and strength of tridimensional periodic lattices

This paper presents a method for the linear analysis of the stiffness and strength of open and closed cell lattices with arbitrary topology. The method hinges on a multiscale approach that separates the analysis of the lattice in two scales. At the macroscopic level, the lattice is considered as a uniform material; at the microscopic scale, on the other hand, the cell microstructure is modelled in detail by means of an in-house finite element solver. The method allows determine the macroscopic stiffness, the internal forces in the edges and walls of the lattice, as well as the global periodic buckling loads, along with their buckling modes. Four cube-based lattices and nine cell topologies derived by Archimedean polyhedra are studied. Several of them are characterized here for the first time with a particular attention on the role that the cell wall plays on the stiffness and strength properties. The method, automated in a computational routine, has been used to develop material property charts that help to gain insight into the performance of the lattices under investigation. © 2012 Elsevier B.V.

Structural optimization of lattice materials

Lattice materials are characterized at the microscopic level by a regular pattern of voids confined by walls. Recent rapid prototyping techniques allow their manufacturing from a wide range of solid materials, ensuring high degrees of accuracy and limited costs. The microstructure of lattice material permits to obtain macroscopic properties and structural performance, such as very high stiffness to weight ratios, highly anisotropy, high specific energy dissipation capability and an extended elastic range, which cannot be attained by uniform materials. Among several applications, lattice materials are of special interest for the design of morphing structures, energy absorbing components and hard tissue scaffold for biomedical prostheses. Their macroscopic mechanical properties can be finely tuned by properly selecting the lattice topology and the material of the walls. Nevertheless, since the number of the design parameters involved is very high, and their correlation to the final macroscopic properties of the material is quite complex, reliable and robust multiscale mechanics analysis and design optimization tools are a necessary aid for their practical application. In this paper, the optimization of lattice materials parameters is illustrated with reference to the design of a bracket subjected to a point load. Given the geometric shape and the boundary conditions of the component, the parameters of four selected topologies have been optimized to concurrently maximize the component stiffness and minimize its mass. Copyright © 2011 by ASME.

滇池水环境中微囊藻毒素的生物降解

利用从滇池蓝藻水华生物量中提取的微囊藻毒素试验溶液,接种滇池沉积物的微生物,研究其在有氧条件下的生物降解过程.结果表明,水体中的微囊藻毒素易被生物降解,其降解反应服从方程C=A/(1+Be-Ct).当温度在12~25℃,加入的沉积物量为1~10g时,藻毒素粗提液的平均降解反应速率为3.181.13d-1,平均半衰期t1/2为2.661.27d,且藻毒素的生物降解速度随反应温度和沉积物量的增加而提高.研究结果还表明,生物降解是去除滇池水环境中微囊藻毒素的一个重要机制.

Stabilization of collective motion in three dimensions: A consensus approach

This paper proposes a methodology to stabilize relative equilibria in a model of identical, steered particles moving in three-dimensional Euclidean space. Exploiting the Lie group structure of the resulting dynamical system, the stabilization problem is reduced to a consensus problem. We first derive the stabilizing control laws in the presence of all-to-all communication. Providing each agent with a consensus estimator, we then extend the results to a general setting that allows for unidirectional and time-varying communication topologies. © 2007 IEEE.

A 40 Gb/s optical bus for optical backplane interconnections

Optical technologies have received large interest in recent years for use in board-level interconnects. Polymer multimode waveguides in particular, constitute a promising technology for high-capacity optical backplanes as they can be cost-effectively integrated onto conventional printed circuit boards (PCBs). This paper presents the first optical backplane demonstrator based on the use of PCB-integrated polymer multimode waveguides and a regenerative shared bus architecture. The backplane demonstrator is formed with commercially-available low-cost electronic and photonic components onto conventional FR4 substrates and comprises two opto-electronic (OE) bus modules interconnected via a prototype regenerator unit. The system enables interconnection between the connected cards over four optical channels, each operating at 10 Gb/s. Bus extension is achieved by cascading OE bus modules via 3R regenerator units, overcoming therefore the inherent limitation of optical bus topologies in the maximum number of cards that can be connected to the bus. Details of the design, fabrication, and assembly of the different parts of this optical bus backplane are presented and related optical and data transmission characterisation studies are reported. The optical layer of the OE bus modules comprises a four-channel three-card waveguide layout that is compatible with VCSEL/PD arrays and ribbon fibres. All on-board optical paths exhibit insertion losses below 13 dB and intra-channel crosstalk lower than -29 dB. The robustness of the signal distribution from the bus inputs to all respective bus output ports in the presence of input misalignment is demonstrated, while 1 dB input alignment tolerances of approximately ±10 μm are obtained. The electrical layer of the OE bus modules comprises the essential driving circuitry for 1×4 VCSEL and PD arrays and the corresponding control and power regulation circuits. The interface between the optical and electrical layers of the bus modules is achieved with simple OE connectors that enable end-fired optical coupling into and out of the on-board polymer waveguides. The backplane demonstrator achieves error-free (BER < 10-12) 10 Gb/s data transmission over each optical channel, enabling therefore, an aggregate interconnection capacity of 40 Gb/s between any connected cards. © 1983-2012 IEEE.

Non-monophyly of fish in the Sinipercidae (Perciformes) as inferred from cytochrome b gene

The sinipercids represent a group of 12 species of freshwater percoid fish, including nine in Siniperca and three species in Coreoperca. Despite several classification attempts and a preliminary molecular phylogeny, the phylogenetic relationships and systematic position of sinipercids remained still unsolved. The complete cytochrome b gene sequences from nine sinipercid species four non-sinipercid fish species were cloned, and a total of 12 cyt b sequences from 10 species of sinipercids and 11 cyt b sequences from 10 species of non-sinipercid fish also in Perciformes were included in the phylogenetic analysis. As expected, the two genera Siniperca and Coreoperca within sinipercids are recovered as monophyletic. However, nine species representing Moronidae, Serranidae, Centropomidae, Acropomatidae, Emmelichtyidae, Siganidae and Centrarchidae included in the present study are all nested between Coreoperca and Siniperca, which provides marked evidence for a non-monophyly of sinipercid fishes. Coreoperca appears to be closest to Centrachus representing the family Centrarchidae. Coreoperca whiteheadi and C. herzi are sibling species, which together are closely related to C. kawamebari. In the Siniperca, the node between S. roulei and the remaining species is the most ancestral, followed by that of S. fortis. S. chuatsi and S. kneri are sibling species, sister to S. obscura. However, the sinipercids do not seem to have a very clear phylogenetic history, for different methods of phylogenetic reconstruction result in different tree topologies, and the only conclusive result in favor of a paraphyletic origin of the two sinipercid genera is the parametric bootstrap test. The paraphyly of Sinipercidae may suggest that the "synapomorphs" such as cycloid scales, upon which this family is based, were independently derived at least twice within sinipercid fishes, and further study should be carried out to include the other two Siniperca species and to incorporate other genes.

Phylogenetic relationships of the Chinese sisorid catfishes: a nuclear intron versus mitochondrial gene approach

Several recent molecular phylogenetic studies of the sisorid catfishes (Sisoridae) have challenged some aspects of their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within this family in these studies highlights the need for additional data and analyses. Here we subjected 15 taxa representing 12 sisorids genera to comprehensive phylogenetic analyses using the second intron of low-copy nuclear S7 ribosomal protein (rpS7) gene and the mitochondrial 16S rRNA gene segments both individually and in combination. The competing sisorid topologies were then tested by using the approximately unbiased (AU) test and the Shimodaira-Hasegawa (SH) test. Our results support previously suggested polyphyly of Pareuchiloglanis. The genus Pseudecheneis is likely to be nested in the glyptosternoids and Glaridoglanis might be basal to the tribe Glyptosternini. However, justified by AU and SH test, the sister-group relationship between Pseudecheneis and the monophyletic glyptosternoids cannot be rejected based on the second intron of rpS7 gene and combined data analyses. It follows that both gene segments are not suitable for resolving the phylogenetic relationships within the sisorid catfishes. Overall, the second intron of rpS7 gene yielded poor phylogenetic performance when compared to 16S rRNA gene, the evolutionary hypothesis of which virtually agreed with the combined data analyses tree. This phenomenon can be explained by the insufficient length and fast saturation of substitutions in the second intron of rpS7 gene, due to substitution patterns such as frequent indels (insertion/deletion events) of bases in the sequences during the evolution.

The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Silurifonnes : Cranoglanididae) and the phylogeny of otophysan fishes

The complete sequence of the 16,539 nucleotide mitochondrial genome from the single species of the catfish family Cranoglanididae, the helmet catfish Cranoglanis bouderius, was determined using the long and accurate polymerase chain reaction (LA PCR) method. The nucleotide sequences of C. bouderius mitochondrial DNA have been compared with those of three other catfish species in the same order. The contents of the C. bouderius mitochondrial genome are 13 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, and a non-coding control region, the gene order of which is identical to that observed in most other vertebrates. Phylogenetic analyses for 13 otophysan fishes were performed using Bayesian method based on the concatenated mtDNA protein-coding gene sequence and the individual protein-coding gene sequence data set. The competing otophysan topologies were then tested by using the approximately unbiased test, the Kishino-Hasegawa test, and the Shimodaira-Hasegawa test. The results show that the grouping ((((Characifonnes, Gymnotiformes), Siluriformes), Cyprinifionnes), outgroup) is the most likely but there is no significant difference between this one and the other alternative hypotheses. In addition, the phylogenetic placement of the family Cranoglanididae among siluriform families was also discussed. (c) 2006 Elsevier B.V. All rights reserved.

Local strain rate and curvature dependences of scalar dissipation rate transport in turbulent premixed flames: A direct numerical simulation analysis

The statistical behaviours of the instantaneous scalar dissipation rate Nc of reaction progress variable c in turbulent premixed flames have been analysed based on three-dimensional direct numerical simulation data of freely propagating statistically planar flame and V-flame configurations with different turbulent Reynolds number Ret. The statistical behaviours of N c and different terms of its transport equation for planar and V-flames are found to be qualitatively similar. The mean contribution of the density-variation term T1 is positive, whereas the molecular dissipation term (-D2) acts as a leading order sink. The mean contribution of the strain rate term T2 is predominantly negative for the cases considered here. The mean reaction rate contribution T3 is positive (negative) towards the unburned (burned) gas side of the flame, whereas the mean contribution of the diffusivity gradient term (D) assumes negative (positive) values towards the unburned (burned) gas side. The local statistical behaviours of Nc, T1, T2, T 3, (-D2), and f(D) have been analysed in terms of their marginal probability density functions (pdfs) and their joint pdfs with local tangential strain rate aT and curvature km. Detailed physical explanations have been provided for the observed behaviour. © 2014 Y. Gao et al.

Taxonomic revision of water-bloom-forming species of oscillatorioid cyanobacteria

A polyphasic approach was used to clarify the taxonomy of the water-bloom-forming oscillatorioid cyanobacteria. Seventy-five strains of oscillatorioid cyanobacteria were characterized by 16S rDNA sequence analysis, DNA base composition, DNA-DNA hybridization, fatty acid composition, phycobilin pigment composition, complementary chromatic adaptation, morphological characters, growth temperature and salinity tolerance. Phylogenetic analysis based on 165 rDNA sequences divided the strains into six groups, all of which were clearly separated from the type species of the genus Oscillatoria, Oscillatoria princeps Gomont NIVA CYA 150. Therefore, these strains should be classified into genera other than Oscillatoria. Groups I-III were closely related to one another and groups IV-VI were distinct from one another and from groups I to III. Group I was further divided into two subgroups, group I-pc, which includes strains containing only phycocyanin (PC), and group I-pe, which includes strains containing large amounts of phycoerythrin (PE) in addition to PC. This phenotypic distinction was supported by DNA-DNA hybridization studies. Based on the properties examined herein and data from traditional, botanical taxonomic studies, the groups and subgroups were classified into single species and we propose either emended or new taxonomic descriptions for Planktothrix agardhii (type strain NIES 204(T)), Planktothrix rubescens (type strain CCAP 1459/22(T)) Planktothrix pseudagardhii sp. nov. (type strain T1-8-4(T)), Planktothrix mougeotii (type strain TR1-5(T)), Planktothricoides raciborskii gen. nov., comb. nov. (type strain NIES 207(T)), Tychonema bourrellyi (type strain CCAP 1459/11B(T)) and Limnothrix redekei (type strain NIVA CYA 277/1(T)).

A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda : Penaeidae) based on mitochondrial dna sequences of selected species from the Indo-West Pacific

Phylogenetic relationships within Metapenaeopsis remain largely unknown. The modern revision of the genus suggests that the shape of the petasma, followed by the presence of a stidulating organ, are the most important distinguishing taxonomic features. In the present study, phylogenetic relationships were studied among seven Metapenaeopsis species from the Indo-West Pacific based on partial sequences of mitochondrial 16S rRNA and cytochrome c oxidase I (COI) genes. Mean sequence divergence was 6.4% for 16S and 15.8% for COI. A strikingly large nucleotide distance (10.0% for 16S and 16.9% for COI) was recorded between M. commensalis, the only Indo-West Pacific species with a one-valved petasma, and the other species with a two-valved petasma. Phylogenetic analyses using neighbor-joining, maximum parsimony, and maximum likelihood generated mostly identical tree topologies in which M. commensalis is distantly related to the other species. Two clades were resolved for the remaining species, one with and the other without a stridulating organ, supporting the main groupings of the recent taxonomic revision. Results of the present study also indicate that the deep-water forms represent a relatively recent radiation in Metapenaeopsis.

Spin-Hall effect in the generalized honeycomb lattice with Rashba spin-orbit interaction

We study the spin-Hall effect in a generalized honeycomb lattice, which is described by a tight-binding Hamiltonian including the Rashba spin-orbit coupling and inversion-symmetry breaking terms brought about by a uniaxial pressure. The calculated spin-Hall conductance displays a series of exact or approximate plateaus for isotropic or anisotropic hopping integral parameters, respectively. We show that these plateaus are a consequence of the various Fermi-surface topologies when tuning epsilon(F). For the isotropic case, a consistent two-band analysis, as well as a Berry-phase interpretation. are also given. (C) 2009 Elsevier B.V. All rights reserved.