Thermodynamic Interpretation of the Meyer-Neldel Rule Explains Temperature Dependence of Ion Diffusion in Silicate Glass.

We study the temperature-dependent diffusion of many types of metal and semimetal ions in soda-lime glass using thermal relaxation ion spectroscopy, a technique that provides an electrical readout of thermally activated diffusion of charge carriers driven by built-in concentration gradients and electric fields. We measure the temperature of the onset of the motion, relevant to the long term storage of radioactive elements. We demonstrate the unique behavior of silver in soda-lime glass, enabling a thermal battery with rapid discharge of stored energy above a threshold temperature. We show that the Meyer-Neldel rule applies when comparisons of temperature-dependent diffusion rates are made between related measurements on one sample or between the same measurements on related samples. The results support a thermodynamic interpretation of the Meyer-Neldel rule as an enthalpy-entropy correlation where the Meyer-Neldel temperature (T_{MN}) is the temperature that enables liquidlike, barrier-free motion of the ions, with an upper limit set by the melting point of the host medium. This interpretation explains the observed reduction in T_{MN} by built-in electric fields in depletion layers and why the upper limit for T_{MN} for all ions is set by the glass transition temperature.

Extending the Debye scattering equation for diffraction from a cylindrically averaged group of atoms: detecting molecular orientation at an interface.

The Debye scattering equation is now over 100 years old and has been widely used to interpret diffraction patterns from randomly oriented groups of atoms. The present work develops and applies a related equation that calculates diffraction intensity from groups of atoms randomly oriented about a fixed axis, a scenario that occurs when molecules are oriented at an interface by the presentation of a binding motif as in antibody binding. Using an example biomolecule, the high level of sensitivity of the diffraction pattern to the orientation of the molecule and to the direction of the incident beam is shown. The use of the method is proposed not only for determining the orientation of molecules in biosensors and at membrane interfaces, but also for determining molecular conformation without the need for crystallization.

Sensory gating in bilayer amorphous carbon memristors.

Multi-state amorphous carbon-based memory devices have been developed that exhibit both bipolar and unipolar resistive switching behaviour. These modes of operation were implemented independently to access multiple resistance states, enabling higher memory density than conventional binary non-volatile memory technologies. The switching characteristics have been further utilised to study synaptic computational functions that could be implemented in artificial neural networks. Notably, paired-pulse inhibition (PPI) is observed at bio-realistic timescales (<100 ms). Devices displaying this rich synaptic behaviour could function as robust stand-alone synapse-inspired memory or be applied as filters for specialised neuromorphic circuits and sensors.

Graphitization of Glassy Carbon after Compression at Room Temperature.

Glassy carbon is a technologically important material with isotropic properties that is nongraphitizing up to ∼3000 °C and displays complete or "superelastic" recovery from large compression. The pressure limit of these properties is not yet known. Here we use experiments and modeling to show permanent densification, and preferred orientation occurs in glassy carbon loaded to 45 GPa and above, where 45 GPa represents the limit to the superelastic and nongraphitizing properties of the material. The changes are explained by a transformation from its sp^{2} rich starting structure to a sp^{3} rich phase that reverts to fully sp^{2} bonded oriented graphite during pressure release.

Predator-prey dynamics stabilised by nonlinearity explain oscillations in dust-forming plasmas.

Dust-forming plasmas are ionised gases that generate particles from a precursor. In nature, dust-forming plasmas are found in flames, the interstellar medium and comet tails. In the laboratory, they are valuable in generating nanoparticles for medicine and electronics. Dust-forming plasmas exhibit a bizarre, even puzzling behaviour in which they oscillate with timescales of seconds to minutes. Here we show how the problem of understanding these oscillations may be cast as a predator-prey problem, with electrons as prey and particles as predators. The addition of a nonlinear loss term to the classic Lotka-Volterra equations used for describing the predator-prey problem in ecology not only stabilises the oscillations in the solutions for the populations of electrons and particles in the plasma but also explains the behaviour in more detail. The model explains the relative phase difference of the two populations, the way in which the frequency of the oscillations varies with the concentration of the precursor gas, and the oscillations of the light emission, determined by the populations of both species. Our results demonstrate the value of adopting an approach to a complex physical science problem that has been found successful in ecology, where complexity is always present.

Reaction paths of phosphine dissociation on silicon (001).

Using density functional theory and guided by extensive scanning tunneling microscopy (STM) image data, we formulate a detailed mechanism for the dissociation of phosphine (PH3) molecules on the Si(001) surface at room temperature. We distinguish between a main sequence of dissociation that involves PH2+H, PH+2H, and P+3H as observable intermediates, and a secondary sequence that gives rise to PH+H, P+2H, and isolated phosphorus adatoms. The latter sequence arises because PH2 fragments are surprisingly mobile on Si(001) and can diffuse away from the third hydrogen atom that makes up the PH3 stoichiometry. Our calculated activation energies describe the competition between diffusion and dissociation pathways and hence provide a comprehensive model for the numerous adsorbate species observed in STM experiments.

Orientation and conformation of anti-CD34 antibody immobilised on untreated and plasma treated polycarbonate.

The conformation and orientation of proteins immobilised on synthetic materials determine their ability to bind their antigens and thereby the sensitivity of the microarrays and biosensors employing them. Plasma immersion ion implantation (PIII) of polymers significantly increases both their wettability and protein binding capacity. This paper addresses the hypothesis that a PIII treated polymer surface modifies the native protein conformation less significantly than a more hydrophobic untreated surface and that the differences in surface properties also affect the protein orientation. To prove this, the orientation and conformation of rat anti-mouse CD34 antibody immobilized on untreated and PIII treated polycarbonate (PC) were investigated using ToF-SIMS and FTIR-ATR spectroscopy. Analysis of the primary structure of anti-CD34 antibody and principal component analysis of ToF-SIMS data were applied to detect the difference in the orientation of the antibody attached to untreated and PIII treated PC. The difference in the antibody conformation was analysed using deconvolution of the Amide I peak (in FTIR-ATR spectra) and curve-fitting. It was found that compared to the PIII treated sample, the antibody immobilized on the untreated PC sample has a secondary structure with a lower fraction of ß-sheets and a higher fraction of α-helices and disordered fragments. Also, it was found that anti-CD34 antibody has a higher tendency to occur in the inactive 'tail-up' orientation when immobilized on an untreated PC surface than on a PIII treated surface. These findings confirm the above hypothesis.

Reaction pathways for pyridine adsorption on silicon (0 0 1).

Density functional theory is used to describe the reactions of chemisorption of pyridine on the silicon (0 0 1) surface. Adsorption energies of six relevant structures, and the activation energies between them are reported. We consider in detail the dative to tight-bridge transition for which conflicting results have been reported in the literature, and provide a description of the formation of inter-row chains observed in high-coverage experiments. We demonstrate that the choice of DFT functional has a considerable effect on the relative energetics and of the four DFT functionals considered, we find that the range-separated hybrid ωB97X-D functional with empirical dispersion provides the most consistent description of the experiment data.

Cluster of differentiation antibody microarrays on plasma immersion ion implanted polycarbonate.

Plasma immersion ion implantation (PIII) modifies the surface properties of polymers, enabling them to covalently immobilize proteins without using linker chemistry. We describe the use of PIII treated polycarbonate (PC) slides as a novel platform for producing microarrays of cluster of differentiation (CD) antibodies. We compare their performance to identical antibody microarrays printed on nitrocellulose-coated glass slides that are currently the industry standard. Populations of leukocytes are applied to the CD microarrays and unbound cells are removed revealing patterns of differentially immobilized cells that are detected in a simple label-free approach by scanning the slides with visible light. Intra-slide and inter-slide reproducibility, densities of bound cells, and limits of detection were determined. Compared to the nitrocellulose-coated glass slides, PIII treated PC slides have a lower background noise, better sensitivity, and comparable or better reproducibility. They require three-fold lower antibody concentrations to yield equivalent signal strength, resulting in significant reductions in production cost. The improved transparency of PIII treated PC in the near-UV and visible wavelengths combined with superior immobilization of biomolecules makes them an attractive platform for a wide range of microarray applications.

Twisted pair of optic fibers for background removal in radiation fields.

In many situations in which an optic fiber carries a signal through a radiation field, an unwanted background signal is produced consisting of fluorescent and/or Cerenkov light. This presents a major problem in the measurement of the light signal, for example, in scintillation dosimetry of medical therapeutic beams. In this paper, we demonstrate a new method of measuring and removing the background signal through the use of a twisted pair of optic fibers. The twisted pair consists of a fiber carrying the scintillation signal that is twisted with a second optic fiber to form a double helix. The two twisted fibers will experience the same radiation environment provided the periodicity of the twist is correlated to the dose rate gradient. An expression for the required twist periodicity is presented. A scintillation dosimeter with a twisted pair optic fiber was tested in a megavoltage beam and found to accurately measure its beam characteristics. The twisted pair approach is not restricted to medical applications and can be used in many situations in which optical signals are carried through radiation fields.

A method to remove residual signals in fibre optic luminescence dosimeters.

Whenever a fibre optic is used to convey a light signal through a radiation field, it is likely that an unwanted background signal will arise from Cerenkov or fluorescent light which will contaminate the signal. In luminescence dosimetry of high energy beams, when a fibre optic is used to convey the signal from the radiation field to the detector, Cerenkov light is the dominant contributor to the background signal and must be corrected for. In this work, a novel method is demonstrated to separate the signal from the unwanted background. A remotely operated shutter is used to block the signal, allowing the residual background in the fibre optic to be quantified. This background is subtracted from the total measurement acquired in a subsequent irradiation, enabling the luminescence signal to be extracted. Two types of shutter mechanism are considered: an electro-mechanical device to intercept the light path and an LCD device to block the light by cross-polarization. Both shutters were characterized and incorporated into a fibre optic dosimetry system used to measure the radiation dose produced by external beam radiation linear accelerators. The dosimeter using each of the shutters in turn was exposed to a 6 MV photon beam to determine their performance, including the measurement of field size dependent output factors. The mechanical shutter determined the output factors to within 0.29% of those measured with an ionization chamber, whereas the LCD shutter gave results that deviated by up to 2.4%. The switching precision of both shutters was good with standard deviations of less than 0.25% and both were able to completely block the light signal when closed. The use of shutters could therefore be applied to any fibre optic based system to quantify and remove a reproducible background arising from any source including ambient, fluorescent and Cerenkov light.

n-type doping of germanium from phosphine: early stages resolved at the atomic level.

To understand the atomistic doping process of phosphorus in germanium, we present a combined scanning tunneling microscopy, temperature programed desorption, and density functional theory study of the reactions of phosphine with the Ge(001) surface. Combining experimental and theoretical results, we demonstrate that PH(2) + H with a footprint of one Ge dimer is the only product of room temperature chemisorption. Further dissociation requires thermal activation. At saturation coverage, PH(2) + H species self-assemble into ordered patterns leading to phosphorus coverages of up to 0.5 monolayers.

Optimization of temporal dose modulation: comparison of theory and experiment.

PURPOSE: To compare theoretical predictions and experimental measurements of cell survival after exposure to two different temporally modulated radiation dose patterns that deliver the same dose in the same overall time. METHODS: The authors derived an analytic expression for the dose protraction factor G in the Lea-Catcheside formalism for cell survival for "triangle" and "V" temporal modulation of dose. These temporal dose patterns were used in experimental clonogenic studies of a melanoma cell line (MM576) and a nonsmall-cell lung cancer line (NCI-H460) that have different alpha, beta, and repair parameters. The overall treatment time and total dose were kept constant. RESULTS: The analytic expressions for G for the two temporal modulations are presented as a function of a single variable, the product of the exposure time, and the repair constant, enabling G to be evaluated for any exposure time and for any cell line. G for the triangle delivery pattern is always the larger. For the MM576 cell line, following a large dose of 6 Gy, a larger survival fraction was found for the V delivery pattern. No difference in survival was observed for lower doses or for the NCI-H460 cell line at any dose. These results are predicted by our theory, using published values of alpha, beta, and repair time within the limits of experimental uncertainty. CONCLUSIONS: The study provides evidence to confirm that cell lines having large beta values exhibit a response that is sensitive to the pattern of dose delivery when the delivery time is comparable with the repair time. It is recommended that the dose delivery pattern be considered in hypofractionated treatments.

Nonequilibrium route to nanodiamond with astrophysical implications.

Nanometer-sized diamond grains are commonly found in primitive chondritic meteorites, but their origin is puzzling. Using evidence from atomistic simulation, we establish a mechanism by which nanodiamonds form abundantly in space in a two-stage process involving condensation of vapor to form carbon onions followed by transformation to nanodiamond in an energetic impact. This nonequilibrium process is consistent with common environments in space and invokes the fewest assumptions of any proposed model. Accordingly, our model can explain nanodiamond formation in both presolar and solar environments. The model provides an attractive framework for understanding noble gas incorporation and explains all key features of meteoritic nanodiamond, including size, shape, and polytype. By understanding the creation of nanodiamonds, new opportunities arise for their exploitation as a powerful astrophysical probe.

Changes in lung tumor shape during respiration.

Evidence that some lung tumors change shape during respiration is derived from respiratory gated CT data by statistical shape modeling and image manipulation. Some tumors behave as rigid objects while others show systematic shape changes. Two views of lung motion are presented to allow analysis of the results. In the first, lung motion is viewed as a wave motion in which inertial effects arising from mass are present and in the second it is a quasistatic motion in which the mass of the lung tissues is neglected. In the first scenario, the extremes of tumor compression and expansion are expected to correlate with maximum upward and downward velocity of the tumor, respectively. In the second, they should occur at end exhale and end inhale, respectively. An observed correlation between tumor strain and tumor velocity provides more support for the first view of lung motion and may explain why previous attempts at observing tumor shape changes during respiration have largely failed. The implications for the optimum gating of radiation therapy are discussed.

Plastic scintillation dosimetry: comparison of three solutions for the Cerenkov challenge.

In scintillation dosimetry, a Cerenkov background signal is generated when a conventional fibre optic is exposed to radiation produced by a megavoltage linear accelerator. Three methods of measuring dose in the presence of Cerenkov background are compared. In the first method, a second background fibre is used to estimate the Cerenkov signal in the signal fibre. In the second method, a colour camera is used to measure the combined scintillation and Cerenkov light in two wavelength ranges and a mathematical process is used to extract the scintillation signal. In the third method, a hollow air core light guide is used to carry the scintillation signal through the primary radiation field. In this paper, the strengths and weaknesses of each dosimetry system are identified and recommendations for the optimum method for common clinical dosimetry situations are made.

Hidden stressors in the clonogenic assay used in radiobiology experiments.

While clonogenic assays are extensively used in radiobiology, there is no widely accepted procedure for choosing the composition of the cell culture media. Cell line suppliers recommend a specific culture medium for each cell line, however a researcher will frequently customize this aspect of the protocol by supplementing the recommended support medium with additives. For example, many researchers add antibiotics, in order to avoid contamination of cells and the consequent loss of data, with little discussion of the influence of the antibiotics on the clonogenic survival of the cells. It is assumed that the effect of any variables in the growth medium on cell survival is taken into consideration by comparing the survival fraction relative to that of controls grown under the same conditions. In the search for better cancer treatment, the effect of various stressors on clonogenic cell survival is under investigation. This study seeks to identify and test potential stressors commonly introduced into the cell culture medium, which may confound the response to radiation.

Comment on 'Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations'.

In a recent publication by Kisi et al (2010 J. Phys.: Condens. Matter 22 162202) the authors present experimentally measured elastic constants for the M(n + 1)AX(n) (MAX) phase, Ti(3)SiC(2), that differ from density functional theory calculations. They then conclude that 'prediction [by ab initio calculation] of the full elasticity tensor for Ti(3)SiC(2) has not been successful'. However the authors do not compare with previous experimental work in which Finkel et al measure the elastic moduli (Finkel et al 2000 J. Appl. Phys. 87 1701). The predictions of ab initio calculations (Yu et al 2005 J. Mater. Res. 20 1180) agree with the measurements of Finkel et al as well as with most other experimentally measured elastic moduli for MAX phases (Cover et al 2008 10 935; Cover et al 2009 J. Phys.: Condens. Matter 21 305403). The unrealistically high value of the C(44) constant obtained by Kisi et al, which would mean that Ti(3)SiC(2) is almost as resistant to shear as diamond, undermines confidence in their results.

Dynamic modeling of lung tumor motion during respiration.

A dynamic finite element model of the lung that incorporates a simplified geometry with realistic lung material properties has been developed. Observations of lung motion from respiratory-gated computed tomography were used to provide a database against which the predictions of the model are assessed. Data from six patients presenting with lung tumors were processed to give sagittal sections of the lung containing the tumor as a function of the breathing phase. Statistical shape modeling was used to outline the diaphragm, the tumor volume and the thoracic wall at each breathing phase. The motion of the tumor in the superior-inferior direction was plotted against the diaphragm displacement. The finite element model employed a simplified geometry in which the lung material fills a rectangular volume enabling two-dimensional coordinates to be used. The diaphragm is represented as a piston, driving the motion. Plots of lung displacement against diaphragm displacement form hysteresis loops that are a sensitive indicator of the characteristics of the motion. The key parameters of lung material that determine the motion are the density and elastic properties of lung material and the airway permeability. The model predictions of the hysteresis behavior agreed well with observation only when lung material is modeled as viscoelastic. The key material parameters are suggested for use as prognostic indicators of the progression of disease and of changes arising from the response of the lung to radiation treatment.

Fizeau interferometer system for fast high resolution studies of spectral line shapes.

A monochromator∕Fizeau interferometer∕intensified CCD camera system is described that was developed for the measurement of the shape of spectral lines that are rapidly time varying. The most important operating parameter that determines the performance of the instrument is the size of the entrance aperture as this determines both the light throughput and the effective interferometer wavelength resolution. This paper discusses, both theoretically and experimentally, the effect of the finite source area on the instrumental resolution to assist in optimizing the choice of this parameter. A second effect that often produces a practical limit to the quality of the spectra is drift of the interferometer plates. Measurements of the shapes of spectral lines of ions and atoms ejected from the cathode spot of continuous and pulsed cathodic arcs are presented to demonstrate the utility of this instrument.