Molecular Computational Elements Encode Large Populations of Small Objects

Since the introduction of molecular computation1, 2, experimental molecular computational elements have grown3, 4, 5 to encompass small-scale integration6, arithmetic7 and games8, among others. However, the need for a practical application has been pressing. Here we present molecular computational identification (MCID), a demonstration that molecular logic and computation can be applied to a widely relevant issue. Examples of populations that need encoding in the microscopic world are cells in diagnostics or beads in combinatorial chemistry (tags). Taking advantage of the small size9 (about 1 nm) and large 'on/off' output ratios of molecular logic gates and using the great variety of logic types, input chemical combinations, switching thresholds and even gate arrays in addition to colours, we produce unique identifiers for members of populations of small polymer beads (about 100 m) used for synthesis of combinatorial libraries10, 11. Many millions of distinguishable tags become available. This method should be extensible to far smaller objects, with the only requirement being a 'wash and watch' protocol12. Our focus on converting molecular science into technology concerning analog sensors13, 14, turns to digital logic devices in the present work.

Fe XIII emission lines in active region spectra obtained with the Solar Extreme-Ultraviolet Research Telescope and Spectrograph

Recent fully relativistic calculations of radiative rates and electron impact excitation cross-sections for FeXIII are used to generate emission-line ratios involving 3s23p2-3s3p3 and 3s23p2-3s23p3d transitions in the 170-225 and 235-450 Å wavelength ranges covered by the Solar Extreme-Ultraviolet Research Telescope and Spectrograph (SERTS). A comparison of these line ratios with SERTS active region observations from rocket flights in 1989 and 1995 reveals generally very good agreement between theory and experiment. Several new FeXIII emission features are identified, at wavelengths of 203.79, 259.94, 288.56 and 290.81 Å. However, major discrepancies between theory and observation remain for several FeXIII transitions, as previously found by Landi and others, which cannot be explained by blending. Errors in the adopted atomic data appear to be the most likely explanation, in particular for transitions which have 3s23p3d1D2 as their upper level. The most useful FeXIII electron-density diagnostics in the SERTS spectral regions are assessed, in terms of the line pairs involved being (i) apparently free of atomic physics problems and blends, (ii) close in wavelength to reduce the effects of possible errors in the instrumental intensity calibration, and (iii) very sensitive to changes in Ne over the range 108-1011cm-3. It is concluded that the ratios which best satisfy these conditions are 200.03/202.04 and 203.17/202.04 for the 170-225 Å wavelength region, and 348.18/320.80, 348.18/368.16, 359.64/348.18 and 359.83/368.16 for 235-450 Å.

Emission lines of [Cl II] in the optical spectra of gaseous nebulae

Recent R-matrix calculations of electron impact excitation rates among the 3s(2)3p(4) levels of Cl II are used to derive the nebular emission-line intensity ratios R-1=I(6161.8 Angstrom)/I(8578.7 Angstrom) and R-2=I(6161.8 Angstrom)/I(9123.6 Angstrom) as a function of electron temperature (T-e) and density (N-e). The ratios are found to be very sensitive to changes in T-e but not N-e for densities lower than 10(5) cm(-3). Hence, they should, in principle, provide excellent optical T-e diagnostics for planetary nebulae. The observed values of R-1 and R-2 for the planetary nebulae NGC 6741 and IC 5117, measured from spectra obtained with the Hamilton echelle spectrograph on the 3 m Shane Telescope, imply temperatures in excellent agreement with those derived from other diagnostic lines formed in the same region of the nebula as [Cl II]. This provides some observational support for the accuracy of the [Cl II] line ratio calculations and hence the atomic data on which they are based. The [Cl II] 8578.7 and 9123.6 Angstrom lines are identified for the first time (to our knowledge) in a high-resolution spectrum of the symbiotic star RR Telescopii, obtained with the University College London Echelle Spectrograph on the 3.9 m Anglo- Australian Telescope. However, the 6161.8 Angstrom feature is unfortunately too weak to be identified in the RR Telescopii observations, consistent with its predicted line strength.

SiIX emission lines in spectra obtained with the Solar EUV Research Telescope and Spectrograph (SERTS)

Theoretical electron-density-sensitive emission line ratios involving 2s(2)2p(2)-2s2p(3) transitions in Si IX between 223 and 350 Angstrom are presented. A comparison of these with an extensive dataset of solar-active-region, quiet-Sun, subflare and off-limb observations, obtained during rocket flights by the Solar EUV Research Telescope and Spectrograph (SERTS), reveals generally very good agreement between theory and experiment. This provides support for the accuracy of the line- ratio diagnostics, and hence the atomic data on which they are based. In particular, the density-sensitive intensity ratio I (258.10 Angstrom)/ I (349.87 Angstrom) offers an especially promising diagnostic for studies of coronal plasmas, as it involves two reasonably strong emission lines and varies by more than an order of magnitude over the useful density range of 10(9)-10(11) cm(-3). The 2s(2)2p(2) S-1(0) - 2s2p(3) P-1(1) transition at 259.77 Angstrom is very marginally identified for the first time in the SERTS database, although it has previously been detected in solar flare observations.

A comparison of theoretical Si VIII emission line ratios with observations from SERTS

Recent R-matrix calculations of electron impact excitation rates in N-like Si VIII are used to derive theoretical emission line intensity ratios involving 2s(2)2p(3)-2s2p(4) transitions in the 216 -320 Angstrom wavelength range. A comparison of these with an extensive dataset of solar active region, quiet- Sun, sub-flare and off-limb observations, obtained during rocket flights of the Solar EUV Research Telescope and Spectrograph (SERTS), indicates that the ratio R-1 = I(216.94 Angstrom)/I(319.84 Angstrom) may provide a usable electron density diagnostic for coronal plasmas. The ratio involves two lines of comparable intensity, and varies by a factor of about 5 over the useful density range of 10(8)-10(11) cm(-3). However R-2 = I(276.85 Angstrom)/I(319.84 Angstrom) and R-3 = I(277.05 Angstrom)/I(319.84 Angstrom) show very poor agreement between theory and observation, due to the severe blending of the 276.85 and 277.05 Angstrom lines with Si VII and Mg VII transitions, respectively, making the ratios unsuitable as density diagnostics. The 314.35 Angstrom feature of Si VIII also appears to be blended, with the other species contributing around 20% to the total line flux.

Extreme-ultraviolet emission lines of S X in solar flare and active region spectra

R-matrix calculations of electron impact excitation rates in N- like S x are used to derive theoretical emission-line intensity ratios involving 2s(2)2p(3)-2s2p(4) transitions in the 189-265 Angstrom wavelength range. A comparison of these with observational data for solar flares and active regions, obtained with the Naval Research Laboratory's S082A spectrograph on board Skylab and the Solar EUV Rocket Telescope and Spectrograph, reveals that many of the S x lines in the spectra are badly blended with emission features from other species. However, the intensity ratios I(228.70 Angstrom)/I(264.24 Angstrom) and I(228.70 Angstrom)/I(259.49 Angstrom) are found to provide useful electron density diagnostics for flares, although the latter cannot be employed for active regions, because of blending of the 259.49 Angstrom line with an unidentified transition in these solar features.

S XI emission lines in active region spectra obtained with the Solar EUV Rocket Telescope and Spectrograph (SERTS)

Theoretical electron density sensitive emission line ratios involving a total of eleven 2s(2)2p(2)-2s2p(3) transitions in S XI between 187 and 292 Angstrom are presented. A comparison of these with solar active region observations obtained during rocket flights by the Solar EUV Rocket Telescope and Spectrograph (SERTS) reveals generally good agreement between theory and experiment. However, the 186.87 Angstrom line is masked by fairly strong Fe XII emission at the same wavelength, while 239.83 Angstrom is blended with an unknown feature, and 285.58 Angstrom is blended with possibly N IV 285.56 Angstrom. In addition, the 191.23 Angstrom line appears to be more seriously blended with an Fe XIII feature than previously believed. The presence of several new S XI lines is confirmed in the SERTS spectra, at wavelengths of 188.66, 247.14 and 291.59 Angstrom, in excellent agreement with laboratory measurements. In particular, the detection of the 2s(2)2p(2) P- 3(1) -2s2p(3) P-3(0,1) transitions at 242.91 Angstrom is the first time (to our knowledge) that this feature has been identified in the solar spectrum. The potential usefulness of the S XI line ratios as electron density diagnostics for the solar transition region and corona is briefly discussed.

An investigation of Fe XV emission lines in solar flare spectra

Previously, large discrepancies have been found between theory and observation for Fe XV emission line ratios in solar flare spectra covering the 224-327 angstrom wavelength range, obtained by the Naval Research Laboratory's S082A instrument on board Skylab. These discrepancies have been attributed to either errors in the adopted atomic data or the presence of additional atomic processes not included in the modelling, such as fluorescence. However our analysis of these plus other S082A flare observations (the latter containing Fe XV transitions between 321-482 angstrom), performed using the most recent Fe XV atomic physics calculations in conjunction with a chianti synthetic flare spectrum, indicate that blending of the lines is primarily responsible for the discrepancies. As a result, most Fe XV lines cannot be employed as electron density diagnostics for solar flares, at least at the spectral resolution of S082A and similar instruments (i.e.similar to 0.1 angstrom). An exception is the intensity ratio I(3s3p P-3(2)-3p(2) P-3(1))/I(3s3p P-3(2)-3p(2) D-1(2))=I(321.8 angstrom)/I(327.0 angstrom), which appears to provide good estimates of the electron density at this spectral resolution.

Computerised Diagnostic Decision Support System for the Classification of Pre-Invasive Cervical Squamous Lesions.

Previous studies have revealed considerable interobserver and intraobserver variation in the histological classification of preinvasive cervical squamous lesions. The aim of the present study was to develop a decision support system (DSS) for the histological interpretation of these lesions. Knowledge and uncertainty were represented in the form of a Bayesian belief network that permitted the storage of diagnostic knowledge and, for a given case, the collection of evidence in a cumulative manner that provided a final probability for the possible diagnostic outcomes. The network comprised 8 diagnostic histological features (evidence nodes) that were each independently linked to the diagnosis (decision node) by a conditional probability matrix. Diagnostic outcomes comprised normal; koilocytosis; and cervical intraepithelial neoplasia (CIN) 1, CIN II, and CIN M. For each evidence feature, a set of images was recorded that represented the full spectrum of change for that feature. The system was designed to be interactive in that the histopathologist was prompted to enter evidence into the network via a specifically designed graphical user interface (i-Path Diagnostics, Belfast, Northern Ireland). Membership functions were used to derive the relative likelihoods for the alternative feature outcomes, the likelihood vector was entered into the network, and the updated diagnostic belief was computed for the diagnostic outcomes and displayed. A cumulative probability graph was generated throughout the diagnostic process and presented on screen. The network was tested on 50 cervical colposcopic biopsy specimens, comprising 10 cases each of normal, koilocytosis, CIN 1, CIN H, and CIN III. These had been preselected by a consultant gynecological pathologist. Using conventional morphological assessment, the cases were classified on 2 separate occasions by 2 consultant and 2 junior pathologists. The cases were also then classified using the DSS on 2 occasions by the 4 pathologists and by 2 medical students with no experience in cervical histology. Interobserver and intraobserver agreement using morphology and using the DSS was calculated with K statistics. Intraobserver reproducibility using conventional unaided diagnosis was reasonably good (kappa range, 0.688 to 0.861), but interobserver agreement was poor (kappa range, 0.347 to 0.747). Using the DSS improved overall reproducibility between individuals. Using the DSS, however, did not enhance the diagnostic performance of junior pathologists when comparing their DSS-based diagnosis against an experienced consultant. However, the generation of a cumulative probability graph also allowed a comparison of individual performance, how individual features were assessed in the same case, and how this contributed to diagnostic disagreement between individuals. Diagnostic features such as nuclear pleomorphism were shown to be particularly problematic and poorly reproducible. DSSs such as this therefore not only have a role to play in enhancing decision making but also in the study of diagnostic protocol, education, self-assessment, and quality control. (C) 2003 Elsevier Inc. All rights reserved.

Phase-resolved emission spectroscopy of a hydrogen rf discharge for the determination of quenching coefficients

Collisional effects can have strong influences on the population densities of excited states in gas discharges at elevated pressure. The knowledge of the pertinent collisional coefficient describing the depopulation of a specific level (quenching coefficient) is, therefore, important for plasma diagnostics and simulations. Phase resolved optical emission spectroscopy (PROES) applied to a capacitively coupled rf discharge excited with a frequency of 13.56 MHz in hydrogen allows the measurement of quenching coefficients for emitting states of various species, particularly of noble gases, with molecular hydrogen as a collision partner. Quenching coefficients can be determined subsequent to electron-impact excitation during the short field reversal phase within the sheath region from the time behavior of the fluorescence. The PROES technique based on electron-impact excitation is not limited â?? in contrast to laser techniques â?? by optical selection rules and the energy gap between the ground state and the upper level of the observed transition. Measurements of quenching coefficients and natural fluorescence lifetimes are presented for several helium (3 1S,4 1S,3 3S,3 3P,4 3S), neon (2p1 ,2p2 ,2p4 ,2p6), argon (3d2 ,3d4 ,3d18 and 3d3), and krypton (2p1 ,2p5) states as well as for some states of the triplet system of molecular hydrogen.

Spectroscopic measurements of phase-resolved electron energy distribution functions in RF-excited discharges

The reliable measurement of the electron energy distribution function (EEDF) of plasmas is one of the most important subjects of plasma diagnostics, because this piece of information is the key to understand basic discharge mechanisms. Specific problems arise in the case of RF-excited plasmas, since the properties of electrons are subject to changes on a nanosecond time scale and show pronounced spatial anisotropy. We report on a novel spectroscopic method for phase- and space-resolved measurements of the electron energy distribution function of energetic (> 12 eV) electrons in RF discharges. These electrons dominate excitation and ionization processes and are therefore of particular interest. The technique is based on time-dependent measurements during the RF cycle of excited-state populations of rare gases admixed in small fractions. These measurements yield � in combination with an analytical model � detailed information on the excitation processes. Phase-resolved optical emission spectroscopy allows us to overcome the difficulties connected with the very low densities (107�109 cm�3) and the transient character of the electrons in the sheath region. The EEDF of electrons accelerated in the sheath region can be described by a shifted Maxwellian with a drift velocity component in direction of the electric field. The method yields the high-energy tail of the EEDF on an absolute scale. The applicability of the method is demonstrated at a capacitively coupled RF discharge in hydrogen.

Direct Observation of strong coupling in a laser-shock compressed plasma

In this Letter we report on a near collective x-ray scattering experiment on shock-compressed targets. A highly coupled Al plasma was generated and probed by spectrally resolving an x-ray source forward scattered by the sample. A significant reduction in the intensity of the elastic scatter was observed, which we attribute to the formation of an incipient long-range order. This speculation is confirmed by x-ray scattering calculations accounting for both electron degeneracy and strong coupling effects. Measurements from rear side visible diagnostics are consistent with the plasma parameters inferred from x-ray scattering data. These results give the experimental evidence of the strongly coupled ionic dynamics in dense plasmas.

Plasma dynamics in an inductively coupled magnetic neutral loop discharge

Magnetic neutral loop discharges (NLDs) can be operated at significantly lower pressures than conventional radio-frequency (rf) inductively coupled plasmas (ICPs). These low pressure conditions are favourable for technological applications, in particular anisotropic etching. An ICP–NLD has been designed providing excellent diagnostics access for detailed investigations of fundamental mechanisms. Spatially resolved Langmuir probe measurements have been performed in the plasma production region (NL region) as well as in the remote application region downstream from the NL region. Depending on the NL gradient two different operation modes have been observed exhibiting different opportunities for control of plasma uniformity. The efficient operation at comparatively low pressures results in ionization degrees exceeding 1%. In this regime neutral dynamics has to be considered and can influence neutral gas and process uniformity. Neutral gas depletion through elevated gas temperatures and high ionization rates have been quantified. At pressures above 0.1 Pa, gas heating is the dominant depletion mechanism. At lower pressures neutral gas is predominantly depleted through high ionization rates and rapid transport of ions by ambipolar diffusion along the magnetic field lines. Non-uniform profiles of the ionization rate can, therefore, result in localized neutral gas depletion and non-uniform processing. We have also investigated the electron dynamics within the radio-frequency cycle using phase resolved optical emission spectroscopy and Thomson scattering. In these measurements electron drift phenomena along the NL torus have been identified.