Roche tomography of the secondary stars in CVs

The secondary stars in cataclysmic variables (CVs) are key to our understanding of the origin, evolution and behaviour of this class of interacting binary. In seeking a fuller understanding of these objects, the challenge for observers is to obtain images of the secondary star. This goal can be achieved through Roche tomography, an indirect imaging technique that can be used to map the Roche-lobe-filling secondary. The review begins with a description of the basic principles that underpin Roche tomography, including methods for determining the system parameters. Finally, we conclude with a look at the main scientific highlights to date, including the first unambiguous detection of starspots on AE Aqr B, and consider the future prospects of this technique.

RU Peg and AE Aqr: two contrasting CVs with one thing in common

Roche tomography is a powerful tool for imaging the surfaces of stars. We have applied it to two contrasting systems, a normal dwarf nova, RU Peg, and the peculiar intermediate polar AE Aqr. Despite these differences, the Roche tomograms of the cool stars in the two systems are remarkably similar. We compare them with tomograms of two other stars, and discuss the differences and similarities. The rotation speed may be critical in determining the surface appearance, and it is strongly recommended that a Roche tomogram be obtained for the bright CV SS Cygni, which would be the fastest-rotating secondary to be studied. In addition, V426 Oph should be re-observed.

Roche Tomography of the Secondary Stars in CVS

The secondary stars in cataclysmic variables (CVs) are key to our understanding of the origin evolution and behaviour of this class of interacting binary. In seeking a fuller understanding of these objects the challenge for observers is to obtain images of the secondary star. This goal can be achieved through Roche tomography an indirect imaging technique that can be used to map the Roche-lobe-filling secondary star. The review begins with a description of the basic principles that underpin Roche tomography including methods for determining the binary system parameters. Noise propagation onto Roche tomograms is also covered. Finally the review concludes with a look at the main scientific highlights to date and the future prospects for Roche tomography

Roche tomography of cataclysmic variables - I. Artefacts and techniques

Roche tomography is a technique used for imaging the Roche-lobe-filling secondary stars in cataclysmic variables (CVs). In order to interpret Roche tomograms correctly, one must determine whether features in the reconstruction are real, or the result of statistical or systematic errors. We explore the effects of systematic errors using reconstructions of simulated data sets, and show that systematic errors result in characteristic distortions of the final reconstructions that can be identified and corrected. In addition, we present a new method of estimating statistical errors on tomographic reconstructions using a Monte Carlo bootstrapping algorithm, and show this method to be much more reliable than Monte Carlo methods which 'jiggle' the data points in accordance with the size of their error bars.

Investigating the Mechanism and Electrode Kinetics of the Oxygen vertical bar Superoxide (O-2 vertical bar O-2(center dot-)) Couple in Various Room-Temperature Ionic Liquids at Gold and Platinum Electrodes in the Temperature Range 298-318 K

The reduction of oxygen was studied over a range of temperatures (298-318 K) in n-hexyltriethylammonium bis(trifluoromethanesulfonyl)imide, [N-6,N-2,N-2,N-2][NTf2], and 1-butyl-2,3-methylimidazolium bis(trifluoromethanesulfonyl)imide, [C(4)dmim][NTf2] on both gold and platinum microdisk electrodes, and the mechanism and electrode kinetics of the reaction investigated. Three different models were used to simulate the CVs, based on a simple electron transfer ('E'), an electron transfer coupled with a reversible homogeneous chemical step ('ECrev') and an electron transfer followed by adsorption of the reduction product ('EC(ads)'), and where appropriate, best fit parameters deduced, including the heterogeneous rate constant, formal electrode potential, transfer coefficient, and homogeneous rate constants for the ECrev mechanism, and adsorption/desorption rate constants for the EC(ads) mechanism. It was concluded from the good simulation fits on gold that a simple E process operates for the reduction of oxygen in [N-6,N-2,N-2,N-2][NTf2], and an ECrev process for [C(4)dmim][NTf2], with the chemical step involving the reversible formation of the O-2(center dot-)center dot center dot center dot [C(4)dmim](+) ion-pair. The E mechanism was found to loosely describe the reduction of oxygen in [N-6,N-2,N-2,N-2][NTf2] on platinum as the simulation fits were reasonable although not perfect, especially for the reverse wave. The electrochemical kinetics are slower on Pt, and observed broadening of the oxidation peak is likely due to the adsorption of superoxide on the electrode surface in a process more complex than simple Langmuirian. In [C(4)dmim][NTf2] the O-2(center dot-) predominantly ion-pairs with the solvent rather than adsorbs on the surface, and an ECrev quantitatively describes the reduction of oxygen on Pt also.

SuperWASP observations of long timescale photometric variations in cataclysmic variables

Aims: We investigated whether the predictions and results of Stanishev et al. (2002, A&A, 394, 625) concerning a possible relationship between eclipse depths in PX And and its retrograde disc precession phase, could be confirmed in long term observations made by SuperWASP. In addition, two further CVs (DQ Her and V795 Her) in the same SuperWASP data set were investigated to see whether evidence of superhump periods and disc precession periods were present and what other, if any, long term periods could be detected. Methods: Long term photometry of PX And, V795 Her and DQ Her was carried out and Lomb-Scargle periodogram analysis undertaken on the resulting light curves. For the two eclipsing CVs, PX And and DQ Her, we analysed the potential variations in the depth of the eclipse with cycle number. Results: The results of our period and eclipse analysis on PX And confirm that the negative superhump period is 0.1417 ± 0.0001d. We find no evidence of positive superhumps in our data suggesting that PX And may have been in a low state during our observations. We improve on existing estimates of the disc precession period and find it to be 4.43 ± 0.05d. Our results confirm the predictions of Stanishev et al. (2002). We find that DQ Her does not appear to show a similar variation for we find no evidence of negative superhumps or of a retrograde disc precession. We also find no evidence of positive superhumps or of a prograde disc precession and we attribute the lack of positive superhumps in DQ Her to be due to the high mass ratio of this CV. We do however find evidence for a modulation of the eclipse depth over a period of 100 days which may be linked with solar-type magnetic cycles which give rise to long term photometric variations. The periodogram analysis for V795 Her detected the likely positive superhump period 0.1165d, however, neither the 0.10826d orbital period nor the prograde 1.53d disc precession period were seen. Here though we have found a variation in the periodogram power function at the positive superhump period, over a period of at least 120 days.

Rapid Surface Plasmon Resonance Immunoassay for the Determination of Deoxynivalenol in Wheat, Wheat Products, and Maize-Based Baby Food

A rapid screening assay (9 min/sample) has been developed and validated for the detection of deoxynivalenol in durum wheat, wheat products, and maize-based baby foods using an SPA biosensor. Through a single laboratory validation, the limits of detection (LOD) for wheat, wheat-based breakfast cereal, and maize-based baby food were 57, 9, and 6 mu g/kg, respectively. Intra-assay and interassay precisions were calculated for each matrix at the maximum and half-maximum European Union regulatory limits and expressed as the coefficient of variation (CV). All CVs fell below 10% with the exception of the between-run CV for breakfast cereal. Recoveries at the concentrations tested ranged from 92 to 115% for all matrices. Action limits of 161, 348, and 1378 mu g/kg were calculated for baby food, wheat-based breakfast cereal, and wheat, respectively, and the linear range of the assay was determined as 250-2000 mu g/kg.

Development of a novel immunobiosensor method for the rapid detection of okadaic acid contamination in shellfish extracts

The mouse bioassay is the methodology that is most widely used to detect okadaic acid (OA) in shellfish samples. This is one of the best-known toxins, and it belongs to the family of marine biotoxins referred to as the diarrhetic shellfish poisons (DSP). Due to animal welfare concerns, alternative methods of toxin detection are being sought. A rapid and specific biosensor immunoassay method was developed and validated for the detection of OA. An optical sensor instrument based on the surface plasmon resonance (SPR) phenomenon was utilised. A polyclonal antibody to OA was raised against OA-bovine thyroglobulin conjugate and OA-N-hydroxy succinimide ester was immobilised onto an amine sensor chip surface. The assay parameters selected for the analysis of the samples were: antibody dilution, 1/750; ratio of antibody to standard, 1:1; volume of sample injected, 25 mu l min(-1); flow rate, 25 mu l min(-1). An assay action limit of 126 ng g(-1) was established by analysing of 20 shellfish samples spiked with OA at the critical concentration of 160 ng g(-1), which is the action limit established by the European Union (EU). At this concentration of OA, the assay delivered coefficient of variations (CVs) of

A simple competitive enzyme immunoassay for the detection of the trypanocidal drug isometamidium

A new competitive enzyme immunoassay technique has been developed for the determination of concentrations of the trypanocidal drug isometamidium chloride (Samorin) in bovine serum. The method has been shown to be highly repeatable and reproducible, and it has several advantages over previous immunoassay techniques for the drug. There are fewer incubation steps overall; microtitre plates may be of coated in batches and stored frozen for future use; and the competition incubation is overnight and is followed only by a brief colour development stage of 10 min. Coefficients of variation (CVs) of duplicate samples were similar to 5%, and mean response variances of untreated cattle (n = 57) were small (CV, 10%). Partitioning of variance showed 77% of this variability to be intrinsic to the samples, and the remaining 23% was due to the procedure. The limit of detection was approximately 0.5 ng ml(-1), which was considered to be satisfactory for the intended use of the method. The drug could be detected in serum of treated cattle for up to 10 weeks following treatment, and determinations showed a high level of reproducibility.

A study of the use of the trimesium salt of glyphosate to desiccate and ret flax and linseed (Linum usitatissimum) and of its effects on the yield of straw, seed and fibre

A replicated field plot experiment was carried out in Northern Ireland in 1996 with flax, cv Ariane, and linseed, cv Flanders, each grown at seed rates of 500, 1000 and 1500 seeds/m(2), in which a comparison was made between netting of the standing crop, following desiccation by the trimesium salt of glyphosate (Touchdown, Zeneca Ltd.), and water or dew retting of the pulled crop. Application at 4 litres/ha on 9 August, 33 days after the mid-point of flowering (MPF), achieved both desiccation and partial retting of the crop within 14 days. Over 16 % clean long fibre was extracted by scutching the stand-netted flax straw, yielding 800 kg/ha fibre, while water retting achieved 20 extraction and 980 kg/ha yield and dew netting 8.5 % and 420 kg/ha respectively. The dew retting was uneven, resulting in high losses during fibre extraction, while water retting for 7 days at 25 degreesC did not achieve complete retting resulting in a high content of woody fragments in the fibre. Fibre yields increased by almost 50 % with the high v. low seed rate. Linseed was less well retted than flax and contained higher levels of impurity in the extracted long fibre which, after retting, yielded 120 to 310 kg/ha at extraction rates of 2.9 % to 7.5 %.

In a second experiment in 1998 flax cvs. Viola and Evelyn were treated with the timesium salt of glyphosate at rates of 2, 4 or 6 litres/ha 10, 20, 30 or 40 days after MPF on 5 July. Viola desiccated satisfactorily at all spray dates with 4 and 6 litres/ha glyphosate. The 20-day treatment desiccated more slowly than the 30-day and the 2 litres/ha rate did not achieve complete desiccation, but the trimesium salt of glyphosate achieved better desiccation at this timing than that found in earlier studies with the original form of glyphosate. Evelyn desiccated more slowly and less evenly than Viola particularly at the 20-day and 40-day timings. Spraying at MPF + 10 days interrupted early development of the seed and fibre significantly reducing yields. Due to slower desiccation the 20-day timing was no better than the 30-day, which was well retted by harvest 44 days after spraying, and gave the highest yield of clean long fibre. The spraying 40 days after MPF was considered too late in the season to be of practical use. It was concluded that retting of standing flax following desiccation with the trimesium salt of glyphosate was more effective than with the earlier formulation and that resting of the standing crop could achieve equivalent or better retting with similar fibre yields to traditional retting methods. The optimum spray timing was found to be about 30 days after MPF with 4 or 6 litres/ha, the lower rate being adequate for glyphosate responsive varieties such as Viola.

Development of a rapid low cost fluorescent biosensor for the detection of food contaminants

A prototype fluorescent based biosensor has been developed for the antibody based detection of food related contaminants. Its performance was characterised and showed a typical antibody binding signal of 200-2000 mV, a short term noise of 9.1 mV, and baseline slope of -0.016 mV/s over 4 h. Bulk signal detection repeatability (n=23) and reproducibility (n=3) were less than 2.4%CV. The biosensor detection unit was evaluated using two food related model systems proving its ability to monitor both binding using commercial products and inhibition through the development of an assay. This assay development potential was evaluated by observing the biosensor's performance whilst appraising several labelled antibody and glass slide configurations. The molecular interaction between biotin and an anti-biotin antibody was shown to be inhibited by 41% due to the presence of biotin in a sample. A food toxin (domoic acid) calibration curve was produced, with %CVs ranging from 2.7 to 7.8%, and a midpoint of approximately 17 ng/ml with further optimisation possible. The ultimate aim of this study was to demonstrate the working principles of this innovative biosensor as a potential portable tool with the opportunity of interchangeable assays. The biosensor design is applicable for the requirements of routine food contaminant analysis, with respect to performance, functionality and cost. (C) 2012 Elsevier B.V. All rights reserved.

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

The not-so-extreme white dwarf of the CV GD 552

GD 552 is a cataclysmic binary which was previously believed to be composed of an M-star and a white dwarf, the latter having an extreme mass of 1.4 solar masses. In a recent paper we showed that this is not compatible with new observational evidence and presented an alternative model in which the white dwarf has a typical mass and the companion is a brown dwarf, making the system a likely member of the elusive group of CVs which have already evolved through minimum orbital period. Here we present additional spectroscopical evidence supporting this conclusion by means of skew mapping.

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Production of a broad specificity antibody for the development and validation of an optical SPR screening method for free and intracellular microcystins and nodularin in cyanobacteria cultures

A highly sensitive broad specificity monoclonal antibody was produced and characterised for microcystin detection through the development of a rapid surface plasmon resonance (SPR) optical biosensor based immunoassay. The antibody displayed the following cross-reactivity: MC-LR 100%; MC-RR 108%; MC-YR 68%; MC-LA 69%; MC-LW 71%; MC-LF 68%; and Nodularin 94%. Microcystin-LR was covalently attached to a CM5 chip and with the monoclonal antibody was employed in a competitive 4min injection assay to detect total microcystins in water samples below the WHO recommended limit (1µg/L). A 'total microcystin' level was determined by measuring free and intracellular concentrations in cyanobacterial culture samples as this toxin is an endotoxin. Glass bead beating was used to lyse the cells as a rapid extraction procedure. This method was validated according to European Commission Decision 96/23/EC criteria. The method was proven to measure intracellular microcystin levels, the main source of the toxin, which often goes undetected by other analytical procedures and is advantageous in that it can be used for the monitoring of blooms to provide an early warning of toxicity. It was shown to be repeatable and reproducible, with recoveries from spiked samples ranging from 74 to 123%, and had % CVs below 10% for intra-assay analysis and 15% for inter-assay analysis. The detection capability of the assay was calculated as 0.5ng/mL for extracellular toxins and 0.05ng/mL for intracellular microcystins. A comparison of the SPR method with LC-MS/MS was achieved by testing six Microcystis aeruginosa cultures and this study yielded a correlation R(2) value of 0.9989.