bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations
Authors: Chang Rakwoo , Ayton Gary S. , Voth Gregory A.
Published: June 2005

A multiscale method is presented to bridge between the atomistic and mesoscopic membrane systems. The atomistic model in this case is the united atom dimyristoylphosphatidylcholine membrane system, although the method is completely general. Atomistic molecular dynamics provides the expansion modulus which is used to parametrize a mesoscopic elastic membrane model. The resulting elastic membrane model, including explicit mesoscopic solvent, shows appropriate static and dynamic undulation behaviors. Large membranes of ∼100nm in length can then be easily simulated using the mesoscopic membrane system. The critical feedback from the mesoscopic system back down to the atomistic-scale system is accomplished by bridging the stress (or surface tension) of a small region in the mesoscopic membrane to the corresponding atomistic membrane system. Because of long length-scale modes of membranes such as undulation and buckling, the local tension responds differently from the frame tension, when subjected to external perturbations. The effect of these membrane modes is shown for the stress response of a local membrane region and therefore the atomistic membrane system. In addition, certain equilibrium static and dynamic properties of stand-alone and multiscale coupled systems are presented for several different membrane sizes. Although static properties such as two-dimensional pair-correlation function and order parameters show no noticeable discrepancy for the different systems, lipid self-diffusion and the rotational relaxation of lipid dipoles have a strong dependence on the membrane size (or long-wavelength membrane motions), which is properly modeled by the present multiscale method.
Formation mechanism and optical properties of nanocrystalline silicon in silicon oxide
Authors: Kim Jong Hoon , Jeon Kyung Ah , Lee Sang Yeol
Published: June 2005

Silicon nanocrystals with diameters ranging from 1.5 to 3 nm were formed on silicon substrates by using a pulsed laser deposition (PLD) followed by annealing and oxidation. The optical and structural properties of the films have been investigated as a function of deposition temperature, annealing, and oxidation process. When the deposition temperature increased, photoluminescence intensity abruptly decreased and peaks showed redshift. Annealing process can reduce the number of defect centers. Oxidation has considerable effect upon the formation and isolation of the nanocrystals. These results suggest that the formation mechanism of Si nanocrystals by using PLD could be explained by three steps of growth, passivating defect centers, and isolation, sequentially.
Coupling between lysozyme and glycerol dynamics: Microscopic insights from molecular-dynamics simulations
Authors: Dirama Taner E. , Carri Gustavo A. , Sokolov Alexei P.
Published: June 2005

We explore possible molecular mechanisms behind the coupling of protein and solvent dynamics using atomistic molecular-dynamics simulations. For this purpose, we analyze the model protein lysozyme in glycerol, a well-known protein-preserving agent. We find that the dynamics of the hydrogen bond network between the solvent molecules in the first shell and the surface residues of the protein controls the structural relaxation (dynamics) of the whole protein. Specifically, we find a power-law relationship between the relaxation time of the aforementioned hydrogen bond network and the structural relaxation time of the protein obtained from the incoherent intermediate scattering function. We demonstrate that the relationship between the dynamics of the hydrogen bonds and the dynamics of the protein appears also in the dynamic transition temperature of the protein. A study of the dynamics of glycerol as a function of the distance from the surface of the protein indicates that the viscosity seen by the protein is not the one of the bulk solvent. The presence of the protein suppresses the dynamics of the surrounding solvent. This implies that the protein sees an effective viscosity higher than the one of the bulk solvent. We also found significant differences in the dynamics of surface and core residues of the protein. The former is found to follow the dynamics of the solvent more closely than the latter. These results allowed us to propose a molecular mechanism for the coupling of the solvent-protein dynamics.
Stokes–Einstein relations for a square-well fluid
Authors: Nigra P. , Evans G. T.
Published: June 2005

A Stokes–Einstein relation, relating the shear viscosity η to the self-diffusion coefficient D, is constructed for a classical fluid subject to an effective two-body intermolecular force, derived from a square-well potential, undergoing dynamics as described by a Smoluchowski equation for pair diffusion. The time correlation functions for η and 1∕D are separated into contributions from delta function, hard-sphere forces, and from delta function, square-well soft forces. Furthermore, D is separated into its two- and three-body time correlation functions, and η into its two- to four-body terms. D shows activated diffusion, as in Arrhenius behavior, and on the level of two-body dynamics, the Dη product adheres to the Stokes–Einstein relation, subject to a small correction for potential softness. Three-body time correlation functions increase D, whereas three- and four-body correlation functions in η are partially offsetting. The deviation of Dη product from the Stokes–Einstein law arises from the three-body time correlations functions in D.
Mixtures of charged colloid and neutral polymer: Influence of electrostatic interactions on demixing and interfacial tension
Authors: Denton Alan R. , Schmidt Matthias
Published: June 2005

The equilibrium phase behavior of a binary mixture of charged colloids and neutral, nonadsorbing polymers is studied within free-volume theory. A model mixture of charged hard-sphere macroions and ideal, coarse-grained, effective-sphere polymers is mapped first onto a binary hard-sphere mixture with nonadditive diameters and then onto an effective Asakura–Oosawa model [S. Asakura and F. Oosawa, J. Chem. Phys. 22, 1255 (1954)]. The effective model is defined by a single dimensionless parameter—the ratio of the polymer diameter to the effective colloid diameter. For high salt-to-counterion concentration ratios, a free-volume approximation for the free energy is used to compute the fluid phase diagram, which describes demixing into colloid-rich (liquid) and colloid-poor (vapor) phases. Increasing the range of electrostatic interactions shifts the demixing binodal toward higher polymer concentration, stabilizing the mixture. The enhanced stability is attributed to a weakening of polymer depletion-induced attraction between electrostatically repelling macroions. Comparison with predictions of density-functional theory reveals a corresponding increase in the liquid-vapor interfacial tension. The predicted trends in phase stability are consistent with observed behavior of protein-polysaccharide mixtures in food colloids.
Reply to “Comment on ‘Analysis of hydroxyl group controlled atomic layer deposition of hafnium oxide from hafnium tetrachloride and water” ’ [J. Appl. Phys. 95, 4777 (2004)]
Authors: Puurunen Riikka L.
Published: June 2005

This response addresses the comments of Alam and Green [J. Appl. Phys. 98, 016101 (2005)] on my article [J. Appl. Phys. 95, 4777 (2004)]. All comments were related to their model [J. Appl. Phys. 94, 3403 (2003)], which I used as a tool for analyzing the origin of substrate-inhibited growth in atomic layer deposition.
Thermal transition measurements of polymer thin films by modulated nanoindentation
Authors: Sills Scott , Fong Hanson , Buenviaje Cynthia , Sarikaya Mehmet , Overney René M.
Published: June 2005

A modulated nanoindentation technique has been developed for thermal transition analysis of polymer thin films. The procedure was applied to glass transition measurements of poly-t-butylacrylate, with results that compare well with shear-modulated force microscopy and differential scanning calorimetry. The advantages of the modulated indentation technique are twofold: (i) it provides in situ experimental access to material properties in nanoscopically confined geometries, and (ii) it incorporates well-defined indenter geometries, which provide a means for quantitative thermorheological analysis that is not available with conventional scanning probe microscopy. The experimental procedure and critical test parameters are detailed.
Near-band-edge slow luminescence in nominally undoped bulk ZnO
Authors: Monteiro T. , Neves A. J. , Carmo M. C. , Soares M. J. , Peres M. , Wang J. , Alves E. , Rita E. , Wahl U.
Published: June 2005

We report the observation of slow emission bands overlapped with the near-band-edge steady-state luminescence of nominally undoped ZnO crystals. At low temperatures the time-resolved spectra are dominated by the emission of several high-energy bound exciton lines and the two-electron satellite spectral region. Furthermore, two donor-acceptor pair transitions at 3.22 and 3.238eV are clearly identified in temperature-dependent time-resolved spectroscopy. These donor-acceptor pairs involve a common shallow donor at 67meV and deep acceptor levels at 250 and 232meV.
Microstructure and ferroelectric properties of low-fatigue epitaxial, all (001)-oriented (Bi,La)4Ti3O12∕Pb(Zr0.4Ti0.6)O3∕(Bi,La)4Ti3O12 trilayered thin films on (001) SrTiO3 substrates
Authors: Bao Dinghua , Zhu Xinhua , Alexe Marin , Hesse Dietrich
Published: June 2005

( Bi , La ) 4 Ti 3 O 12 ( BLT ) ∕ Pb ( Zr , Ti ) O 3 ( PZT ) ∕ ( Bi , La ) 4 Ti 3 O 12 trilayered ferroelectric thin films were epitaxially grown by pulsed laser deposition onto (001) SrTiO3 (STO) substrates with and without SrRuO3 (SRO) bottom electrodes. From x-ray pole figures and electron-diffraction patterns, the epitaxial relationships between BLT, PZT, SRO, and STO were identified to be BLT(001)‖PZT(001)‖SRO(001)‖SrTiO3(001); BLT[110]‖PZT[100]‖SRO[100]‖SrTiO3[100]. Cross-sectional transmission electron microscopy investigations revealed that 90° ferroelectric domain boundaries lying on {110} planes are present in the PZT layer, with an average domain width of 20nm and an average spacing of 120nm. These long 90° ferroelectric domains, as a rule having nucleated at the bottom of the PZT layer, extend to the top of the latter. The thin films have sharp BLT/PZT interfaces and a very flat surface. The remanent polarization and coercive field were determined as 13.9μC∕cm2 and 72.9kV∕cm, respectively, indicating that the epitaxial, all (001)-oriented trilayered thin films have rather good ferroelectric properties, although single epitaxial (001)-oriented BLT films are usually not favored for application due to their very poor ferroelectric properties. The thin films showed a high fatigue resistance at least up to 1010 switching pulse cycles, confirming that such a trilayered structure effectively shows the fatigue-free behavior of BLT.
High magnetoresistive sensitivity in electrodeposited FeCoNi∕Cu multilayers
Authors: Gong Jie , Butler William H. , Zangari Giovanni
Published: June 2005

Fe Co Ni ∕ Cu multilayers with large magnetoresistive sensitivity at low field have been electrodeposited on n-type Si from a single electrolyte by modulating the deposition potential. Dissolution of the ferromagnetic (FM) layer during copper deposition was minimized and interface sharpness was improved by monitoring the current transients during the transition from FM to Cu deposition and using these data to fine tune the Cu deposition potential and Fe2+ concentration in the electrolyte. Using optimal processing parameters, a maximum giant magnetoresistance (GMR) ratio above 9% could be obtained. Maximum GMR sensitivity of over 0.11%∕Oe was achieved in the field range 5–15Oe.
Analytical solutions for a spherical particle near a wall in axisymmetrical polynomial creeping flows
Authors: Pasol L. , Chaoui M. , Yahiaoui S. , Feuillebois F.
Published: June 2005

Analytical solutions are presented for axisymmetric creeping flows around a spherical particle near a wall, when the unperturbed flow velocity varies as polynomial with the coordinates. The perturbed fluid velocity and pressure are calculated directly with the method of bipolar coordinates. They are obtained with a 10−16 precision, even for small gaps of the order of 10−6 sphere radius. For a constant unperturbed flow, the problem is equivalent to that of a sphere moving perpendicularly to a wall in a fluid at rest. An alternative indirect solution for the fluid velocity and pressure is obtained in this case from the solution of Brenner [Chem. Eng. Sci. 16, 242 (1961)] and Maude [Brit. J. Appl. Phys. 12, 293 (1961)] for the stream function. For a small gap between the sphere and the wall, the values of the pressure are compatible with the ones from the lubrication approximation but are systematically larger; this may be important for applications. Calculations are also performed when the unperturbed flow velocity is a polynomial of degree 2 and 3 in the coordinates, viz., for different types of stagnation point flows. Various flow structures are obtained, depending on the particle to wall distance. When the sphere approaches the wall, there is an increasing number of nested toroidal eddies, providing a link between the case of a single toroidal eddy when the sphere is far from the wall and the infinite set of Moffatt eddies in the gap between bodies in contact. The flow structure is analogous to that for two equal spheres in a uniform flow field, cf. Davis, O’Neill, Dorrepaal, and Ranger [J. Fluid Mech. 77, 625 (1976)]. Precise results for the force on the sphere are provided.
Interpretation of enhancement factor in nonplanar field emitters
Authors: Smith R. C. , Forrest R. D. , Carey J. D. , Hsu W. K. , Silva S. R. P.
Published: June 2005

A comparison of the field emission properties of exposed nanotubes lying on a tipped carbon nanorope, with the emission properties from a sharpened iron tip of similar dimensions is performed. By varying the electrode separation it is observed that the threshold field for emission for both structures decreases as the electrode separation initially increases; however, for sufficiently large electrode separations, the threshold field is observed to reach an asymptotic value. Our results show that the field enhancement factor is fundamentally associated with the electrode separation, and depending on the experimental conditions in order to obtain a true value for electric field a set of alternative definitions for enhancement factors is required. We further confirm our experimental synopsis by simulation of the local electrostatic field which gives results similar to those obtained experimentally.
Electro-optic characteristics and switching principle of a single-cell-gap transflective liquid-crystal display associated with in-plane rotation of liquid crystal driven by a fringe-field
Authors: Song J. H. , Lim Y. J. , Lee M.-H. , Lee S. H. , Shin S. T.
Published: June 2005

A single-gap transflective liquid-crystal (LC) display associated with in-plane rotation of the LC director was designed. In the device, a fringe electric field drives to rotate a homogeneously aligned LC in plane to optimize polarization efficiency. Rotating degrees of the LC director, 22.5° and 45° were required in both reflective and transmissive regions, respectively. In the device, the cell gap was the same for both regions, and a dark state was irrespective of the cell retardation value at normal direction, which was highly important in massive fabrications. The switching principle and electro-optic characteristics of the device are reported herein.
Low-power, multiport, ultrafast, parametric switching in cascaded waveguide couplers
Authors: Schiek Roland , Iwanow Robert , Stegeman George , Pertsch Thomas , Lederer Falk , Min Yoo Hong , Sohler Wolfgang
Published: June 2005

We explore an approach to multiport, phase-insensitive all-optical switching of milliwatt power signals based on linear coupling in cascaded directional couplers and on nonlinear parametric gain via the second-order nonlinearity. For the basic unit, a two-core coupler, we experimentally demonstrated ultrafast transparent switching of 1550nm signals triggered by 5-ps-long control pulses at ≈775nm with a peak power of 1.3W. Theoretically, we show that this concept has the potential for terabit/s switching with a few picojoules control energy and without pulse degradation.
Contrast Configuration Influences Grouping in Apparent Motion
Authors: Ma-Wyatt Anna , Clifford Colin W G , Wenderoth Peter
Published: June 2005

We investigated whether the same principles that influence grouping in static displays also influence grouping in apparent motion. Using the Ternus display, we found that the proportion of group motion reports was influenced by changes in contrast configuration. Subjects made judgments of completion of these same configurations in a static display. Generally, contrast configurations that induced a high proportion of group motion responses were judged as more ‘complete’ in static displays. Using a stereo display, we then tested whether stereo information and T-junction information were critical for this increase in group motion. Perceived grouping was consistently higher for same contrast polarity configurations than for opposite contrast polarity configurations, regardless of the presence of stereo information or explicit T-junctions. Thus, while grouping in static and moving displays showed a similar dependence on contrast configuration, motion grouping showed little dependence on stereo or T-junction information.
Enhancement of grape berry weight induced by an ethanol spray four weeks before harvest and effects of a night spray at an earlier date
Authors: Chervin C. , Savocchia S. , Krstic M. , Serrano E. , van Heeswijck R.
Published: June 2005

Spraying aqueous solutions of ethanol (between 2.5 and 10%, v/v) 1 month before harvest has been shown to increase berry weight of Cabernet Sauvignon by about 10% at harvest compared with controls sprayed with water. These observations were made in France and in Australia. The increase in berry weight was not associated with significant changes in total soluble solids. Additional measurements showed that spraying aqueous solutions of ethanol onto the berry surface 1 month before harvest had only small effects on the colour of berry skin extracts. In another trial, spraying ethanol at night 1 month earlier than other trials lead to a slight increase in the colour of the skin extracts. Optimisation of the spraying conditions is discussed.
Modelling the bi-peak lactation curves of summer calvers in New Zealand dairy farm systems
Authors: Beukes P. C. , Thorrold B. S. , Wastney M. E. , Palliser C. C. , Macdonald K. A. , Bright K. P. , Lancaster J. A. S. , Palmer C. A. J. , Auldist M. J.
Published: June 2005

New Zealand dairy cows traditionally calve in late winter, so their peak lactation demands are met by the increased growth of pasture in spring, and they are dried off in autumn before the decreased growth in winter. Financial premiums are offered to encourage farmers to produce milk in winter by calving cows in summer or autumn (out-of-season calving). This requires farming systems that can feed lactating cows in winter, which may include extra silages and fertilisers. The associated extra costs must be weighed against the value of the winter premium.
This paper assesses the ability of Dexcel’s Whole Farm Model (WFM) to simulate out-of-season calving by comparing the model output with the observed data from an out-of-season calving trial run at Dexcel’s No. 2 dairy in Hamilton from 1998 to 2001. Trial data showed the typical lactation curve for July calvers with 1 peak in early lactation, whereas for January calvers the curve was atypical with a lower peak in early lactation and a second peak in late lactation. July and January calvers were described in the animal metabolic submodel (‘Molly’) at the start of the simulations by using observed liveweights at the beginning of the season and estimated peak daily milk yields. The management submodel used best-practice policies and the pasture submodel was driven by actual climate data. The WFM with an unmodified ‘Molly’ (without the photoperiod effect) did not predict the flatter bi-peak lactation curves of the January calvers. Driving forces responsible for the differences in the shape of lactation curves were identified and a sine function reflecting the photoperiod effect on lactation hormones was incorporated into ‘Molly’. This reduced the mean prediction error of milk yields for January calvers from 46 to 19%, and for July calvers, from 19 to 15%. The modified ‘Molly’ also showed potential to predict the atypical lactation curves of October and April calvers.
After evaluating the WFM, farm systems can be simulated by altering factors such as stocking rate, fertiliser quantity and timing, and proportion of the herd calving out of season. Model output can be used for cost–benefit analysis of a wide variety of potential systems.
Sex and porcine somatotropin impact on variation in growth performance and back fat thickness
Authors: Dunshea F. R.
Published: June 2005

Managing variation in carcass weight and composition is an enormous challenge for the pig producer. A means of improving growth performance and reducing back fat is porcine exogenous somatotropin (pST) treatment. It is possible that this technology may also reduce variation in these important growth and carcass parameters. This study was conducted to provide data on the effect of sex and pST on variation in growth and carcass characteristics. Sixteen on-farm studies involving 1495 pigs were conducted in various states within Australia. On each farm, groups of pigs were randomly assigned within sex to one of 2 management regimes (control or pST regime). The control regime consisted of feeding the typical finisher diet used on that farm while the pST regime involved feeding the typical grower diet used on the farm combined with daily injections of pST (5 mg/day). Data from individual pigs were collated and the summary descriptive statistics derived for each treatment group on each farm were then analysed. Daily liveweight gain was lower and feed conversion ratio (FCR) and back fat at the P2 site were higher in gilts than in boars. The pST regime increased average mean daily gain and reduced feed intake, FCR and back fat at the P2 site. The coefficient of variation (CV) around live daily gain was lower in gilts than in boars (19.3 v 22.3% for gilts and boars, respectively, P<0.001) and in pigs treated with the pST regime (22.1 v. 19.9% for the control and pST regimes, respectively, P<0.001). The CV around liveweight was higher in the control boars than in any of the other treatment groups as indicated by the main (P<0.001) and interactive (P<0.001) effects of both sex and pST regime. The coefficient of variation around P2 was reduced by pST (16.2 v. 14.2%, P<0.001) but was not different between gilts and boars. There was an interaction (P = 0.025) between pST regime and sex with the average kurtosis for the P2 distribution positive in gilts treated with pST but slightly negative in all the other groups. The distributions were on average skewed to the right, particularly in gilts (P = 0.017) and in pigs treated with pST (P<0.001). In conclusion, these data demonstrate that as well as improving mean final liveweight and P2 back fat, pST treatment can also reduce variation in these key production parameters that form the basis for economic returns to the producer.
The apparent ileal digestibility of amino acids in common vetch (Vicia sativa cv. Morava)
Authors: Collins C. L. , Dunshea F. R. , Henman D. J. , McCauley I. , King R. H.
Published: June 2005

A total in of 12 entire male pigs were selected at about 32 kg liveweight and randomly allocated to 2 dietary treatments containing 0 and 400 g/kg vetch (Vicia sativa cv. Morava), respectively. Pigs were offered 1.3 kg of their respective diets for 15 days. The diets also contained 0.2 g/kg n-hextriacontane as an indigestible marker to allow the determination of amino acid digestibility at the terminal ileum. On day 15, pigs were anaesthetised, a ventral abdominal midline incision made and samples of faecal and ileal digesta collected. Samples were used to measure the apparent ileal digestibility of the amino acids in the diets and the amino acid digestibility in vetch was calculated by difference. The apparent ileal digestibilities of lysine, threonine, methionine and arginine were 71.4, 53.5, 52.1 and 78.4%, respectively. The apparent ileal digestibility of the amino acids in vetch were relatively high and suggest common vetch (Vicia sativa cv. Morava) has the potential to be a viable alternative protein source for use in pig diets.
Effect of hedging and tree removal on productivity of crowding macadamia orchards
Authors: McFadyen L. M. , Morris S. G. , McConchie C. A. , Oldham M. A.
Published: June 2005

Hedging and 25% tree removal were investigated in a 6-year study as strategies to manage tree crowding in mature macadamia orchards. The trial orchard comprised 9-year-old macadamia (Macadamia integrifolia Maiden and Betche) trees, cultivar Kau (HAES 344), planted at 7 × 3.5 m and which had formed a hedgerow. In the hedged treatment, both sides of the hedgerow were lightly pruned annually with a mechanical hedger. In the tree removal treatment, 25% of trees were thinned out by removing every second tree in every second row. Hedging reduced yield in years 5 and 6 after the start of hedging, by 14 and 21%, respectively. Over 6 years, average yield reduction due to hedging was only 4%. Tree removal reduced yield/ha by 17% in the year immediately after thinning and this effect gradually reduced to 11% over the next 5 years as trees grew into the available space. Over 6 years, average yield reduction due to tree removal was 15%. The economic implications of the different patterns of yield reduction are discussed. Nuts dropped earlier in the tree removal treatment but there were no effects of hedging or tree removal on kernel recovery, unsound kernel or grade 1 kernel.
The evolutionary relationships of North American Diplous Motschulsky (Coleoptera:Carabidae:Patrobini) inferred from morphological and molecular evidence
Authors: Marek Paul E. , Kavanaugh David H.
Published: June 2005

Individuals of the ground beetle genus Diplous Motschulsky, 1850 occur in riparian areas predominately throughout boreal North America and Asia. In order to infer the species phylogeny of the North American Diplous, we examined 97 morphological characters (56 quantitative characters and 41 qualitative characters) and 458 bp of the mitochondrial cytochrome oxidase subunit I region. We used the four North American species, four Palearctic species, and one undescribed species of a closely related genus to test the monophyly and the direction of character state change in North American Diplous. Overall, we found that North American Diplous appear to represent a monophyletic group, but that the morphological and molecular evidence did not support the same relationships in the placement of one of the species. We found that the total evidence trees agreed most with biogeography and considerations of accelerated morphological evolution. In this paper, we present a morphological phylogenetic tree, a molecular phylogenetic tree, a total evidence phylogenetic tree, a species key, species diagnoses, and a distribution map of Nearctic Diplous.
When and where did troidine butterflies (Lepidoptera : Papilionidae) evolve? Phylogenetic and biogeographic evidence suggests an origin in remnant Gondwana in the Late Cretaceous
Authors: Braby Michael F. , Trueman John W. H. , Eastwood Rod
Published: June 2005

The age, geographic origin and time of major radiation of the butterflies (Hesperioidea + Papilionoidea + Hedyloidea) are largely unknown. The general modern view is that butterflies arose during the Late Jurassic/Cretaceous in the southern hemisphere (southern Pangea/Gondwana before continental breakup), but this is not universally accepted, and is a best guess based largely on circumstantial evidence. The extreme paucity of fossils and lack of modern, higher-level phylogenies of extant monophyletic groups have been major impediments towards determining reliable estimates of either their age or geographic origin. Here we present a phylogenetic and historical biogeographic analysis of a higher butterfly taxon, the swallowtail tribe Troidini. We analysed molecular data for three protein-encoding genes, mitochondrial ND5 and COI–COII, and nuclear EF–1α, both separately and in combination using maximum parsimony (with and without character weighting and transition/transversion weighting), maximum likelihood and Bayesian methods. Our sample included representatives of all 10 genera of Troidini and distant ingroup taxa (Baroniinae, Parnassiinae, Graphiini, Papilionini), with Pieridae as outgroup. Analysis of the combined dataset (4326 bp; 1012 parsimony informative characters) recovered the Troidini as a well supported monophyletic group and the monophyly of its two subtribes, Battina and Troidina. The most parsimonious biogeographic hypothesis suggests a southern origin of the tribe in remnant Gondwana (Madagascar–Greater India–Australia–Antarctica–South America) sometime after the rifting and final separation of Africa in the Late Cretaceous (<90 Mya). Although an ancient vicariance pattern is proposed, at least four relatively recent dispersal/extinction events are needed to reconcile anomalies in distribution, most of which can be explained by geological and climatic events in South-east Asia and Australia during the late Tertiary. Application of a molecular clock based on a rate smoothing programme to estimate various divergence times based on vicariance events, revealed two peculiarities in our biogeographic vicariance model that do not strictly accord with current understanding of the temporal breakup of Gondwana: (1) the troidine fauna of Greater India did not become isolated from Gondwana (Antarctica) until the end of the Cretaceous (c. 65 Mya), well after Madagascar separated from Greater India (84 Mya); and (2) the faunas of Greater India, Australia and South America diverged simultaneously, also at the K/T boundary. A recent published estimate of the time (31 Mya) of divergence between Cressida Swainson (Australia) and Euryades Felder & Felder (South America) is shown to be in error.
Highly sensitive DNA fingerprinting of orchid pollinaria remnants using AFLP
Authors: Indsto James O. , Weston Peter H. , Clements Mark A. , Whelan Robert J.
Published: June 2005

Numerous Australian terrestrial orchid species in the genus Diuris may be pollinated by food source mimicry. In our field studies, direct observations of orchid–pollinator interactions were rare, but native bees were frequently captured carrying orchid pollinaria, or pollinaria remnants. Sometimes, pollinaria remnants were minimal and included only the viscidium, a sticky pad that was often highly persistent. Confirmation of such tissue as being of orchid source, and attributing them to a particular species can aid pollination studies. DNA-based methods that may identify more or less intact orchid pollinaria are available, but extremely small and degraded samples can pose technical challenges. We have developed an AFLP protocol for such difficult samples that offers some significant advantages over direct PCR-based analysis. We simulated AFLP profiling of very low-DNA samples using DNA template from serial dilutions. A DNA sample range from 6.4 picograms to at least as high as 100 nanograms (15 500-fold range) all yielded AFLP fingerprints. The practical application of this inherent sensitivity of AFLP is demonstrated by the identification of remnants of orchid pollinaria sampled from bees, presented here as a case study. It is expected that this approach will find many applications where sample DNA is limiting, or possibly where pollen of similar appearance may comprise species mixtures.
Analyzing a bioterror attack on the food supply: The case of botulinum toxin in milk
Authors: Wein Lawrence M. , Liu Yifan
Published: June 2005

We developed a mathematical model of a cows-to-consumers supply chain associated with a single milk-processing facility that is the victim of a deliberate release of botulinum toxin. Because centralized storage and processing lead to substantial dilution of the toxin, a minimum amount of toxin is required for the release to do damage. Irreducible uncertainties regarding the dose–response curve prevent us from quantifying the minimum effective release. However, if terrorists can obtain enough toxin, and this may well be possible, then rapid distribution and consumption result in several hundred thousand poisoned individuals if detection from early symptomatics is not timely. Timely and specific in-process testing has the potential to eliminate the threat of this scenario at a cost of <1 cent per gallon and should be pursued aggressively. Investigation of improving the toxin inactivation rate of heat pasteurization without sacrificing taste or nutrition is warranted.
A modular microfluidic architecture for integrated biochemical analysis
Authors: Shaikh Kashan A. , Ryu Kee Suk , Goluch Edgar D. , Nam Jwa-Min , Liu Juewen , Thaxton C. Shad , Chiesl Thomas N. , Barron Annelise E. , Lu Yi , Mirkin Chad A. , Liu Chang
Published: June 2005

Microfluidic laboratory-on-a-chip (LOC) systems based on a modular architecture are presented. The architecture is conceptualized on two levels: a single-chip level and a multiple-chip module (MCM) system level. At the individual chip level, a multilayer approach segregates components belonging to two fundamental categories: passive fluidic components (channels and reaction chambers) and active electromechanical control structures (sensors and actuators). This distinction is explicitly made to simplify the development process and minimize cost. Components belonging to these two categories are built separately on different physical layers and can communicate fluidically via cross-layer interconnects. The chip that hosts the electromechanical control structures is called the microfluidic breadboard (FBB). A single LOC module is constructed by attaching a chip comprised of a custom arrangement of fluid routing channels and reactors (passive chip) to the FBB. Many different LOC functions can be achieved by using different passive chips on an FBB with a standard resource configuration. Multiple modules can be interconnected to form a larger LOC system (MCM level). We demonstrated the utility of this architecture by developing systems for two separate biochemical applications: one for detection of protein markers of cancer and another for detection of metal ions. In the first case, free prostate-specific antigen was detected at 500 aM concentration by using a nanoparticle-based bio-bar-code protocol on a parallel MCM system. In the second case, we used a DNAzyme-based biosensor to identify the presence of Pb
2+
(lead) at a sensitivity of 500 nM in <1 nl of solution.
Aeolian transport with collisional suspension
Authors: Pasini José Miguel , Jenkins James T
Published: June 2005

This paper considers the aeolian transport of sand by a wind so strong that the concentration of sand near the bed makes collisions between grains inevitable. It employs an improved model of such a collisional flow which includes turbulent suspension, viscous dissipation and new top boundary conditions that are validated by numerical calculations of collisionless trajectories.
The Ferrier Lecture 2004 What can transcranial magnetic stimulation tell us about how the brain works?
Authors: Cowey Alan
Published: June 2005

Transcranial magnetic stimulation (TMS) is a technique whereby parts of the cerebral cortex and underlying white matter can be excited by a brief electrical current induced by a similarly brief, rapidly fluctuating magnetic field which is itself produced by rapidly discharging a current through an insulated coil held against the scalp. When combined with magnetic resonance structural and functional images of the subject's brain, the stimulation can be directed at specific cortical areas. Over a period of only 15 years, TMS has revealed hitherto unsuspected aspects of brain function, such as the role of distant parts of the brain in recovery from stroke, and has helped to resolve several previously intractable disputes, such as the neuronal basis of conscious awareness. This article describes and discusses the origins and nature of TMS, its applications and limitations, and its especial usefulness in conjunction with other techniques of evaluating or imaging brain activity.
Dicer-1 and R3D1-L catalyze microRNA maturation in Drosophila
Authors: Jiang Feng , Ye Xuecheng , Liu Xiang , Fincher Lauren , McKearin Dennis , Liu Qinghua
Published: June 2005

In Drosophila melanogaster, Dicer-2/R2D2 and Dicer-1 generate small interfering RNA (siRNA) and microRNA (miRNA), respectively. Here we identify a novel dsRNA-binding protein, which we named R3D1-L, that forms a stable complex with Dicer-1 in vitro and in vivo. While depletion of R3D1-L by RNAi causes accumulation of precursor miRNA (pre-miRNA) in S2 cells, recombinant R3D1-L enhances miRNA production by Dicer-1 in vitro. Furthermore, R3D1 deficiency causes miRNA-generating defect and severe sterility in male and female flies. Therefore, R3D1-L functions in concert with Dicer-1 in miRNA biogenesis and is required for reproductive development in Drosophila.
Identifying Plasmodium falciparum merozoite surface antigen 3 (MSP3) protein peptides that bind specifically to erythrocytes and inhibit merozoite invasion
Authors: Rodríguez Luis E. , Curtidor Hernando , Ocampo Marisol , Garcia Javier , Puentes Alvaro , Valbuena John , Vera Ricardo , López Ramses , Patarroyo Manuel E.
Published: June 2005

Receptor–ligand interactions between synthetic peptides and normal human erythrocytes were studied to determine Plasmodium falciparum merozoite surface protein‐3 (MSP‐3) FC27 strain regions that specifically bind to membrane surface receptors on human erythrocytes. Three MSP‐3 protein high activity binding peptides (HABPs) were identified; their binding to erythrocytes became saturable, had nanomolar affinity constants, and became sensitive on being treated with neuraminidase and trypsin but were resistant to chymotrypsin treatment. All of them specifically recognized 45‐, 55‐, and 72‐kDa erythrocyte membrane proteins. They all presented α‐helix structural elements. All HABPs inhibited in vitro P. falciparum merozoite invasion of erythrocytes by ∼55%–85%, suggesting that MSP‐3 protein's role in the invasion process probably functions by using mechanisms similar to those described for other MSP family antigens.
Mycobacterium tuberculosis serine/threonine kinases PknB, PknD, PknE, and PknF phosphorylate multiple FHA domains
Authors: Grundner Christoph , Gay Laurie M. , Alber Tom
Published: June 2005

The physiologic roles and the substrates of the Mycobacterium tuberculosis (Mtb) serine/threonine kinases are largely unknown. Here, we report six novel interactions of PknB, PknD, PknE, and PknF with the Forkhead‐Associated (FHA) domains of Rv0020c and the putative ABC transporter Rv1747. Purified PknB and PknF kinase domains phosphorylated multiple FHA‐domain proteins in vitro. Although they remain to be verified in vivo, these reactions suggest a web of interactions between STPKs and FHA domains.
Crystallographic studies on acyl ureas, a new class of glycogen phosphorylase inhibitors, as potential antidiabetic drugs
Authors: Oikonomakos Nikos G. , Kosmopoulou Magda N. , Chrysina Evangelia D. , Leonidas Demetres D. , Kostas Ioannis D. , Wendt K. Ulrich , Klabunde Thomas , Defossa Elisabeth
Published: June 2005

Acyl ureas were discovered as a novel class of inhibitors for glycogen phosphorylase, a molecular target to control hyperglycemia in type 2 diabetics. This series is exemplified by 6‐{2,6‐Dichloro‐ 4‐[3‐(2‐chloro‐benzoyl)‐ureido]‐phenoxy}‐hexanoic acid, which inhibits human liver glycogen phosphorylase a with an IC50 of 2.0 μM. Here we analyze four crystal structures of acyl urea derivatives in complex with rabbit muscle glycogen phosphorylase b to elucidate the mechanism of inhibition of these inhibitors. The structures were determined and refined to 2.26Å resolution and demonstrate that the inhibitors bind at the allosteric activator site, where the physiological activator AMP binds. Acyl ureas induce conformational changes in the vicinity of the allosteric site. Our findings suggest that acyl ureas inhibit glycogen phosphorylase by direct inhibition of AMP binding and by indirect inhibition of substrate binding through stabilization of the T′ state.
Design of improved membrane protein production experiments: Quantitation of the host response
Authors: Bonander Nicklas , Hedfalk Kristina , Larsson Christer , Mostad Petter , Chang Celia , Gustafsson Lena , Bill Roslyn M.
Published: June 2005

Eukaryotic membrane proteins cannot be produced in a reliable manner for structural analysis. Consequently, researchers still rely on trial‐and‐error approaches, which most often yield insufficient amounts. This means that membrane protein production is recognized by biologists as the primary bottleneck in contemporary structural genomics programs. Here, we describe a study to examine the reasons for successes and failures in recombinant membrane protein production in yeast, at the level of the host cell, by systematically quantifying cultures in high‐performance bioreactors under tightly‐defined growth regimes. Our data show that the most rapid growth conditions of those chosen are not the optimal production conditions. Furthermore, the growth phase at which the cells are harvested is critical: We show that it is crucial to grow cells under tightly‐controlled conditions and to harvest them prior to glucose exhaustion, just before the diauxic shift. The differences in membrane protein yields that we observe under different culture conditions are not reflected in corresponding changes in mRNA levels ofFPS1, but rather can be related to the differential expression of genes involved in membrane protein secretion and yeast cellular physiology.
Lessons from the design of a novel atomic potential for protein folding
Authors: Chen William W. , Shakhnovich Eugene I.
Published: June 2005

We investigate all‐atom potentials of mean force for estimating free energies in protein folding and fold recognition. We search through the space potentials and design novel atomic potentials with a random mixing approximation and a contact‐correlated Gaussian approximation of decoy states. We show that the two derived potentials are highly correlated, supporting the use of the random energy model as an accurate statistical description of protein conformational states. The novel atomic potentials perform well in a Z‐score and fold decoy recognition test. Furthermore, the designed atomic potential performs slightly and significantly better than atomic potentials derived under a quasi‐chemical assumption. While accounting for connectivity correlations between atom types does not improve the performance of the designed potential, we show these correlations lead to ambiguities in the distribution of energetic contributions for atoms on the same residue. Within the confines of the model then, many potentials may exist which stabilize all native folds in subtly different ways. Comparison of different protein conformations under the various atomic potentials reveals both a remarkable degree of correspondence in the estimated free energies and a remarkable degree of correspondence in the identity of the contacts types that make the dominant contributions to the estimated free energies. This consistency may be interpreted as a sign that the design procedure is extracting physically meaningful quantities.
Rv0216, a conserved hypothetical protein from Mycobacterium tuberculosis that is essential for bacterial survival during infection, has a double hotdog fold
Authors: Castell Alina , Johansson Patrik , Unge Torsten , Jones T. Alwyn , Bäckbro Kristina
Published: June 2005

The Mycobacterium tuberculosis genome contains about 4000 genes, of which approximately a third code for proteins of unknown function or are classified as conserved hypothetical proteins. We have determined the three‐dimensional structure of one of these, the rv0216 gene product, which has been shown to be essential for M. tuberculosis growth in vivo. The structure exhibits the greatest similarity to bacterial and eukaryotic hydratases that catalyse the R‐specific hydration of 2‐enoyl coenzyme A. However, only part of the catalytic machinery is conserved in Rv0216 and it showed no activity for the substrate crotonyl‐CoA. The structure of Rv0216 allows us to assign new functional annotations to a family of seven other M. tuberculosis proteins, a number if which are essential for bacterial survival during infection and growth.
Characterization of peptide folding nuclei by hydrogen/deuterium exchange‐mass spectrometry
Authors: Li Xue , Hood Robin J. , Wedemeyer William J. , Watson J. Throck
Published: June 2005

Covalently linked pairs of well‐chosen peptides can be good model systems for protein folding studies because they can adopt stable secondary, side‐chain, and tertiary structure under certain conditions. We demonstrate a method for characterizing the structure in such peptide pairs by hydrogen/deuterium exchange of individual amide groups analyzed by collision‐induced dissociation tandem mass spectrometry, in concert with circular dichroism spectroscopy. We apply the method to two peptides (and their three possible pairs) from bovine pancreatic trypsin inhibitor to address specific hypotheses regarding the stabilization of local secondary structure by long‐range interactions.
TNF-α and intPLA2 genes' polymorphism in anorexia nervosa
Authors: Slopien Agnieszka , Rybakowski Filip , Dmitrzak-Weglarz Monika , Czerski Piotr , Hauser Joanna , Komorowska-Pietrzykowska Renata , Rajewski Andrzej
Published: June 2005

Objective:

The aim of this study was the assessment of −308G/A tumor necrosis factor (TNF)-α gene polymorphism and intPLA2 gene polymorphism in patients with anorexia nervosa (AN) and healthy controls.

Subjects:

We studied 91 non-related patients with AN and 144 healthy women (blood donors and students). The mean age of women from study group was 18.22 years (SD ± 3.13 years) and from control group was 31.71 years (SD ± 8.22).

Methods:

Gene polymorphisms were studied with the use of polymerase chain reaction-restriction fragment length polymorphism method. TNF-α gene polymorphism consists of G/A substitution in −308 promoter region. IntPLA2 gene polymorphism is related to intron 1, in which restrictive region is found and recognized by BanI enzyme.

Results:

We did not obtain statistically significant differences in the frequency of genotypes and alleles of −308G/A TNF-α polymorphism between the study and control groups (genotypes: P = 0.106, alleles: P = 0.076). We did analogous analysis in the restrictive and bulimic subgroups. We did not observe statistically relevant differences in the frequency of genotypes (P = 0.700) and alleles (P = 0.305). We did not obtain statistically relevant difference in the frequency of genotypes and alleles of intPLA2 gene between the study group and controls (genotypes: P = 0.300, alleles: P = 0.331). We did analogous analysis in both subgroups of AN. We did not observe statistically relevant differences in the frequency of genotypes (P = 0.344) and alleles (P = 0.230).

Conclusions:

There was no statistically relevant trend for the association between TNF-α polymorphism and AN. We did not find association between studied polymorphism of intPLA2 gene and risk of AN.