Efficient sampling of atomic configurational spaces.

We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling (AIP Conf. Proc. 2004, 395; J. Bayesian Anal. 2006, 1, 833) and allows us to explore the entire potential energy surface (PES) efficiently in an unbiased way. The algorithm has two parameters which directly control the trade-off between the resolution with which the space is explored and the computational cost. We demonstrate the use of nested sampling on Lennard-Jones (LJ) clusters. Nested sampling provides a straightforward approximation for the partition function; thus, evaluating expectation values of arbitrary smooth operators at arbitrary temperatures becomes a simple postprocessing step. Access to absolute free energies allows us to determine the temperature-density phase diagram for LJ cluster stability. Even for relatively small clusters, the efficiency gain over parallel tempering in calculating the heat capacity is an order of magnitude or more. Furthermore, by analyzing the topology of the resulting samples, we are able to visualize the PES in a new and illuminating way. We identify a discretely valued order parameter with basins and suprabasins of the PES, allowing a straightforward and unambiguous definition of macroscopic states of an atomistic system and the evaluation of the associated free energies.

Tree-Structured Stick Breaking Processes for Hierarchical Data

Many data are naturally modeled by an unobserved hierarchical structure. In this paper we propose a flexible nonparametric prior over unknown data hierarchies. The approach uses nested stick-breaking processes to allow for trees of unbounded width and depth, where data can live at any node and are infinitely exchangeable. One can view our model as providing infinite mixtures where the components have a dependency structure corresponding to an evolutionary diffusion down a tree. By using a stick-breaking approach, we can apply Markov chain Monte Carlo methods based on slice sampling to perform Bayesian inference and simulate from the posterior distribution on trees. We apply our method to hierarchical clustering of images and topic modeling of text data.

Study of the electric loading aspects of the BDFM using a lumped parameter thermal model

Details of a lumped parameter thermal model for studying thermal aspects of the frame size 180 nested loop rotor BDFM at the University of Cambridge are presented. Predictions of the model are verified against measured end winding and rotor bar temperatures that were measured with the machine excited from a DC source. The model is used to assess the thermal coupling between the stator windings and rotor heating. The thermal coupling between the stator windings is assessed by studying the difference of the steady state temperatures of the two stator end windings for different excitations. The rotor heating is assessed by studying the temperatures of regions of interest for different excitations.

Novel cathelicidin-derived antimicrobial peptides from Equus asinus

In the present study, EA-CATH1 and EA-CATH2 were identified from a constructed lung cDNA library of donkey (Equus asinus) as members of cathelicidin-derived antimicrobial peptides, using a nested PCR-based cloning strategy. Composed of 25 and 26 residues, respectively, EA-CATH1 and EA-CATH2 are smaller than most other cathelicidins and have no sequence homology to other cathelicidins identified to date. Chemically synthesized EA-CATH1 exerted potent antimicrobial activity against most of the 32 strains of bacteria and fungi tested, especially the clinically isolated drug-resistant strains, and minimal inhibitory concentration values against Gram-positive bacteria were mostly in the range of 0.3-2.4 mu g center dot mL-1. EA-CATH1 showed an extraordinary serum stability and no haemolytic activity against human erythrocytes in a dose up to 20 mu g center dot mL-1. CD spectra showed that EA-CATH1 mainly adopts an alpha-helical conformation in a 50% trifluoroethanol/water solution, but a random coil in aqueous solution. Scanning electron microscope observations of Staphylococcus aureus (ATCC2592) treated with EA-CATH1 demonstrated that EA-CATH could cause rapid disruption of the bacterial membrane, and in turn lead to cell lysis. This might explain the much faster killing kinetics of EA-CATH1 than conventional antibiotics revealed by killing kinetics data. In the presence of CaCl2, EA-CATH1 exerted haemagglutination activity, which might potentiate an inhibition against the bacterial polyprotein interaction with the host erythrocyte surface, thereby possibly restricting bacterial colonization and spread.

Rapid detection of white spot syndrome virus (WSSV) of Penaeus monodon by latex agglutination test using monoclonal antibodies

Latex beads were sensitized with monoclonal antibodies (MAb) rose against VP28 of WSSV. The optimum concentration of MAb required to sensitize the latex beads was 125 µg/ml. The sensitized latex beads were used to detect WSSV from PCR-positive stomach tissue homogenates obtained from infected shrimp. Stomach tissue homogenates from WSSV-infected shrimp agglutinated the sensitized latex beads within 10 minutes, while uninfected samples did not produce any agglutination, although non-specific agglutinations were observed in some samples. The analytical sensitivity, analytical specificity, diagnostic sensitivity and diagnostic specificity of the (LAT) agglutination test were assessed. The analytical sensitivity of the test was 40 ng of purified WSSV (2 µg/ml). The sensitized latex beads did not agglutinate with normal shrimp tissue or MBV-infected tissue homogenate. The test has a diagnostic sensitivity of 70 and 45%, respectively, compared to single-step and nested PCR. The diagnostic specificity of the test was 82%. This test is a simple and rapid on-farm test which can be used to corroborate clinical signs for the detection of WSSV in grow-out ponds.

Phylogenetic relationships of the mustache toads inferred from mtDNA sequences

Species of the genus Vibrissaphora are unique among all annurans in that males exhibit external cornified spines in the maxillary region during the breeding season. They were separated from species of the genus Leptobrachium based on this unique character. We construct a phylogeny using the 16S, ND4, and cytochrome b mitochondrial genes of 42 individuals from eight species of Vibrissaphora and five species of Leptobrachium from mainland China, Southeast Asia, and Hainan Island. Species of both Oreolalax and Scutiger were used as outgroups. The results indicate that: L. huashen and L. chapaense form a clade that is nested within Vibrissaphora, and L. hainanense is the sister taxon to the clade comprising all Vibrissaphora plus L. chapaense and L. huashen; V. boringiae is grouped with a clade consisting of V. leishanensis, V. liui, and V. yaoshanensis; and V. yaoshanensis is a species separate from V. liui. We propsed taxonomix changes that reflect these findings. Also based on the resulting phylogenetic trees, we propose that the mustache toads originated in the trans-Himalayan region of southwest China, and that the evolution of maxillary spines, large body size, and reverse sexual size dimorphism in these frogs was influenced by intrasexual selection due to adopting a resource-defense polygyny matting system.

Characterization of acid-sensing ion channels in dorsal horn neurons of rat spinal cord

Acid-sensing ion channels (ASICs) are ligand-gated cation channels activated by extracellular protons. In periphery, they contribute to sensory transmission, including that of nociception and pain. Here we characterized ASIC-like currents in dorsal horn neurons of the rat spinal cord and their functional modulation in pathological conditions. Reverse transcriptase-nested PCR and Western blotting showed that three ASIC isoforms, ASIC1a, ASIC2a, and ASIC2b, are expressed at a high level in dorsal horn neurons. Electrophysiological and pharmacological properties of the proton-gated currents suggest that homomeric ASIC1a and/or heteromeric ASIC1a + 2b channels are responsible for the proton-induced currents in the majority of dorsal horn neurons. Acidification-induced action potentials in these neurons were compatible in a pH-dependent manner with the pH dependence of ASIC-like current. Furthermore, peripheral complete Freund's adjuvant-induced inflammation resulted in increased expression of both ASIC1a and ASIC2a in dorsal horn. These results support the idea that the ASICs of dorsal horn neurons participate in central sensory transmission/modulation under physiological conditions and may play important roles in inflammation-related persistent pain.

Derivation of a vector model for a Brushless Doubly-Fed Machine with multiple loops per nest

The paper presents a vector model for a Brushless Doubly-Fed Machine (BDFM). The BDFM has 4 and 8 pole stator windings and a nested-loop rotor cage. The rotor cage has six nests equally spaced around the circumference and each nest comprises three loops. All the rotor loops are short circuited via a common end-ring at one end. The vector model is derived based on the electrical equations of the machine and appropriate vector transformations. In contrast to the stator, there is no three phase circuit in the rotor. Therefore, the vector transformations suitable for three phase circuits can not be utilised for the rotor circuit. A new vector transformation is employed for the rotor circuit quantities. The approach presented in this paper can be extended for a BDFM with any stator poles combination and any number of loops per nest. Simulation results from the model implemented in Simulink are presented. © 2008 IEEE.

Stable operation of the Brushless Doubly-Fed Machine (BDFM)

A simple method of controlling the Brushless Doubly-Fed Machine (BDFM) is presented. The controller comprises two Proportional-Integral (PI) modules and requires only the rotor speed feedback. The machine model and the control system are developed in MATLAB. Both simulation and experimental results are presented. The performance of the system is presented in the motoring and generating operations. The experimental tests included in this paper were carried out on a 180 frame size BDFM with a nested-loop rotor. © 2007 IEEE.

Characterising rotors for brushless doubly-fed machines (BDFM)

The brushless doubly fed machine (BDFM) is a robust alternative to the doubly fed induction generator (DFIG) which is widely used in wind turbines but suffers from failures associated with its brushes and sliprings. The rotor plays an important part in a BDFM, coupling the two stator fields. To date, the nested loop has been almost exclusively used in modern BDFMs, but this approach is not ideally suited to large machines in which a form wound rotor is likely to be preferable from a manufacturing point of view. This paper gives a comparative study of two rotor windings. The performance of the rotors has been predicted from theory for a frame size 160 BDFM. Actual rotors have been built, using identical rotor laminations, and tested, giving results which accord well with predictions. The results give insight into the design issues of rotors both from electrical and manufacturing viewpoints. ©2010 IEEE.

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.

Local Frustration Determines Molecular and Macroscopic Helix Structures

The effect of displaying cytochromes from an amyloid fibre is modelled as perturbation of -strands in a bilayer of helical -sheets, thereby explaining the spiral morphology of decorated amyloid and the dynamic response of morphology to cytochrome conformation. The morphology of the modelled fibre, which consists of minimal energy assemblies of rigid building blocks containing two anisotropic interacting units, depends primarily on the rigid constraints between units rather than the soft interactions between them. The framework is a discrete version of the bilayered frustration principle that drives morphology in Bauhinia seedpods. We show that self-assembly of frustrated long range structures can occur if the building blocks themselves are internally frustrated, e.g. amyloid morphology is governed by the conformation of the misfolded protein nucleating the fibre. Our model supports the idea that any peptide sequence can form amyloid if bilayers can form first, albeit stabilised by additional material such as chaperones or cytochromes. Analysis of experimentally derived amyloid structures supports our conclusions and suggests a range of frustration effects, which natural amyloid fibres may exploit. From this viewpoint, amyloid appears as a molecular example of a more general universal bilayered frustration principle, which may have profound implications for materials design using fibrous systems. Our model provides quantitative guidance for such applications. The relevance to longer length scales was proved by designing the morphology of a series of macroscopic magnetic stacks. Finally, this work leads to the idea of mixing controlled morphologically defined species to generate higher-order assembly and complex functional behaviour. The systematic kinking of decorated fibres and the nested frustration of the Bauhinia seed pod are two outstanding examples.

Dynamic modelling of the brushless doubly fed machine

A coupled-circuit model for the brushless doubly fed machine (BDFM) has been developed. The transformation of the model into the d-q axis form, ultimately in a synchronous reference frame in which machine currents and voltages have constant values in the steady state, has been carried out. A model-reduction technique is presented, which gives a concise representation of the 'nested-loop' rotor design using a single d-q pair. These models have been experimentally verified and give a convenient and accurate way of calculating the dynamic behaviour of a BDFM. The ability to represent the BDFM with a single d-q pair considerably simplifies the design of suitable controllers. © The Institution of Engineering and Technology 2013.

Novel nanostructured carbon nanotube electron sources

In this chapter, we present a review of our continuing efforts toward the development of discrete, low-dimensional nanostructured carbon-based electron emitters. Carbon nanotubes and nanofibers, herein referred to simply as CNTs, are one-dimensional carbon allotropes formed from cylindrically rolled and nested graphene sheets, have diameters between 1 and 500 nm and lengths of up to several millimeters, and are perfect candidates for field emission (FE) applications. By virtue of their extremely strong sp2 C-C bonding, intrinsic to the graphene hexagonal lattice, CNTs have demonstrated impressive chemical inertness, unprecedented thermal stabilities, significant resistance to electromigration, and exceptionally high axial current carrying capacities, even at elevated temperatures. These near ideal cold cathode electron emitters have incredibly high electric field enhancing aspect ratios combined with virtual point sources of the order of a few nanometers in size. The correct integration and judicious development of suitable FE platforms based on these extraordinary molecules is critical and will ultimately enable enhanced technologies. This chapter will review some of the more recent platforms, devices and structures developed by our group, as well as our contributions towards the development of industry-scalable technologies for ultra-high-resolution electron microscopy, portable x-ray sources, and flexible environmental lighting technologies. © 2012 by Pan Stanford Publishing Pte. Ltd. All rights reserved.

Population genetic structure and geographical differentiation of the Chinese catfish Hemibagrus macropterus (Siluriformes, Bagridae): Evidence for altered drainage patterns

National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120]