Working group report: Collider Physics

This is summary of the activities of the working group on collider physics in the IXth Workshop on High Energy Physics Phenomenology (WHEPP-9) held at the Institute of Physics, Bhubaneswar, India in January 2006. Some of the work subsequently done on these problems by the subgroups formed during the workshop is included in this report.     

Fluorescent sensor for Cu2+ with a tunable emission wavelength

A concept of fluorescent metal ion sensing with an easily tunable emission wavelength is presented and its principle demonstrated by detection of Cu(2+). A fluorescein dye was chemically modified with a metal chelating group and then attached to the terminus of ss-DNA. This was combined with a complementary ss-DNA modified with another fluorescent dye (ATTO 590), emitting at a longer wavelength. In the assembled duplex, fluorescence resonance energy transfer (FRET) between the fluorescein donor (excited at 470 nm) and the ATTO 590 acceptor (emitting at 624 nm) is observed. Proper positioning within the rigid DNA double helix prevents intramolecular contact quenching of the two dyes. Coordination of paramagnetic Cu(2+) ions by the chelating unit of the sensor results in direct fluorescence quenching of the fluorescein dye and indirect (by loss of FRET) quenching of the ATTO 590 emission at 624 nm. As a result, emission of the acceptor dye can be used for monitoring of the concentration of Cu(2+), with a 20 nM detection limit. The emission wavelength is readily tuned by replacement of ATTO-DNA by other commercially available DNA-acceptor dye conjugates. Fluorescent metal ion sensors emitting at >600 nm are very rare. The possibility of tuning the emission wavelength is important with respect to the optimization of this sensor type for application to biological samples, which usually show broad autofluorescence at <550 nm.     

Capillary array scanner for time-resolved detection and identification of fluorescently labelled DNA fragments

The first capillary array scanner for time-resolved fluorescence detection in parallel capillary electrophoresis based on semiconductor technology is described. The system consists essentially of a confocal fluorescence microscope and a x,y-microscope scanning stage. Fluorescence of the labelled probe molecules was excited using a short-pulse diode laser emitting at 640 nm with a repetition rate of 50 MHz. Using a single filter system the fluorescence decays of different labels were detected by an avalanche photodiode in combination with a PC plug-in card for time-correlated single-photon counting (TCSPC). The time-resolved fluorescence signals were analyzed and identified by a maximum likelihood estimator (MLE). The x,y-microscope scanning stage allows for discontinuous, bidirectional scanning of up to 16 capillaries in an array, resulting in longer fluorescence collection times per capillary compared to scanners working in a continuous mode. Synchronization of the alignment and measurement process were developed to allow for data acquisition without overhead. Detection limits in the subzeptomol range for different dye molecules separated in parallel capillaries have been achieved. In addition, we report on parallel time-resolved detection and separation of more than 400 bases of single base extension DNA fragments in capillary array electrophoresis. Using only semiconductor technology the presented technique represents a low-cost alternative for high throughput DNA sequencing in parallel capillaries.     

Observation of Unusual Molecular Diffusion Behaviour below the Lower Critical Solution Temperature of Water/2‐Butoxyethanol Mixtures by using Fluorescence Correlation Spectroscopy

The effect of solute affinity on solute diffusion in binary liquids well below the lower critical solution temperature (LCST) was studied by using fluorescence correlation spectroscopy. We measured the hydrodynamic radii of a hydrophobic and an amphiphilic fluorescent dye under systematic variation of the relative molar fractions of water/2‐butoxyethanol and, for comparison, of water/methanol mixtures, which do not show phase separation. We found that the apparent hydrodynamic radius of the hydrophobic dye almost doubled in water/2‐butoxyethanol, whereas it remained largely unchanged for the amphiphilic dye and in water/methanol mixtures. Our results indicate that the translational diffusion of solutes is influenced by transient local solution structures, even at temperatures well below the LCST. We conclude that, even far below LCST, different solutes can experience different environments in binary liquid mixtures depending on both the solute and solvent properties, all of which impact their reactivity.     

On the singularity of Green's tensor for a perfectly conducting semi-infinite cone

This paper is intended to clarify a misunderstanding concerningthe source singularity of the electric Green's tensor for aperfectly conducting semi-infinite cone of circular cross-section.Tai's series expansion of the Green's tensor is known to lacka singular term at the source region. Jones has reconstructedthe solution to this problem and has pointed out the differencebetween his result and that of Tai. The aim of our paper isto demonstrate that, although Jones's closed-form solution iscorrect, there is a mistake in his comparison with Tai's seriessolution. We conclude that one of the two additional singularterms that Jones claims as missing from Tai's formula must beomitted. Besides, we compare Jones's closed-form solution withSmyshlyaev's solution to the very same problem. We concludethat the magnetic field expressions given by Jones and Smyshlyaevcoincide, but a singular term is missing from Smyshlyaev's expressionfor the electric field.