Fractal analysis of CE CT lung tumours images

AIM The fractal dimension (FD) of a structure provides a measure of its complexity. This pilot study aims to determine FD values for lung cancers visualised on Computed Tomography (CT) and to assess the potential for tumour FD measurements to provide an index of tumour aggression. METHOD Pre-and post-contrast CT images of the thorax acquired from 15 patients with lung cancers of greater than 10mm were transformed to fractal dimension images using a box-counting algorithm at various scales. A region of interest (ROI) was determined covering tumour locations, which were more apparent on FD images as compared to images before processing. The average tumour FD (FDavg) was computed and compared with the intensity average before FD processing. FD values were correlated with 2 markers of tumour aggression: tumour stage and tumour uptake of fluorodeoxyglucose (FDG) as determined by Positron Emission Tomography. RESULTS For pre-contrast images, the tumour FDavg correlated with tumour stage (r = 0.537, p = 0.0387) and FDG uptake (r= 0.64, p< 0.001). FDavg decreased following contrast enhancement for most tumours. CONCLUSION Fractal analysis of CT images of lung tumours could potentially provide additional information about likely tumour aggression and so impact on clinical management decisions and choice of treatment

Molecule survival in magnetized protostellar disk winds. II. Predicted H2O line profiles versus Herschel/HIFI observations

We investigate whether the broad wings of H2O emission identified with Herschel towards low-mass Class 0 and Class 1 protostars may be consistent with an origin in a dusty MHD disk wind, and the constraints it would set on the underlying disk properties. We present synthetic H2O line profiles predictions for a typical MHD disk wind solution with various values of disk accretion rate, stellar mass, extension of the launching area, and view angle. We compare them in terms of line shapes and intensities with the HIFI profiles observed by the WISH Key Program. We find that a dusty MHD disk wind launched from 0.2--0.6 AU AU to 3--25 AU can reproduce to a remarkable degree the observed shapes and intensities of the broad H2O component, both in the fundamental 557 GHz line and in more excited lines. Such a model also readily reproduces the observed correlation of 557 GHz line luminosity with envelope density, if the infall rate at 1000 AU is 1--3 times the disk accretion rate in the wind ejection region. It is also compatible with the typical disk size and bolometric luminosity in the observed targets. However, the narrower line profiles in Class 1 sources suggest that MHD disk winds in these sources, if present, would have to be slower and/or less water rich than in Class 0 sources. In conclusion, MHD disk winds appear as a valid (though not unique) option to consider for the origin of the broad H2O component in low-mass protostars. ALMA appears ideally suited to further test this model by searching for resolved signatures of the warm and slow wide-angle molecular wind that would be predicted.Comment: accepted for publication in A&

Random Walk Model on a Hyper-Spherical Lattice

We use a one-dimensional random walk on $D$-dimensional hyper-spheres to determine the critical behavior of statistical systems in hyper-spherical geometries. First, we demonstrate the properties of such walk by studying the phase diagram of a percolation problem. We find a line of second and first order phase transitions separated by a tricritical point. Then, we analyze the adsorption-desorption transition for a polymer growing near the attractive boundary of a cylindrical cell membrane. We find that the fraction of adsorbed monomers on the boundary vanishes exponentially when the adsorption energy decreases towards its critical value. We observe a crossover phenomenon to an area of linear growth at energies of the order of the inverse cell radius.Comment: to appear in NPB Proc. Suppl. of LATTICE'94, 3 pages, ps-file uuencoded, 2 figures included, NO-NUM-

Temporal evolution of magnetic molecular shocks I. Moving grid simulations

We present time-dependent 1D simulations of multifluid magnetic shocks with chemistry resolved down to the mean free path. They are obtained with an adaptive moving grid implemented with an implicit scheme. We examine a broad range of parameters relevant to conditions in dense molecular clouds, with preshock densities between 10^3 and 10^5 cm-3, velocities between 10 and 40 km/s, and three different scalings for the transverse magnetic field: B=0,0.1,1 \mu G \sqrt{n.cm3}. We first use this study to validate the results of Chi\`eze, Pineau des For\^ets & Flower (1998), in particular the long delays necessary to obtain steady C-type shocks, and we provide evolutionary time-scales for a much greater range of parameters. We also present the first time-dependent models of dissociative shocks with a magnetic precursor, including the first models of stationary CJ shocks in molecular conditions. We find that the maximum speed for steady C-type shocks is reached before the occurrence of a sonic point in the neutral fluid, unlike previously thought. As a result, the maximum speed for C-shocks is lower than previously believed. Finally, we find a large amplitude bouncing instability in J-type fronts near the H2 dissociation limit (u ~ 25-30 km/s), driven by H2 dissociation/reformation. At higher speeds, we find an oscillatory behaviour of short period and small amplitude linked to collisional ionisation of H. Both instabilities are suppressed after some time when a magnetic field is present. In a companion paper, we use the present simulations to validate a new semi-analytical construction method for young low-velocity magnetic shocks based on truncated steady-state models.Comment: A&A in pres

Mie plasmons: modes volumes, quality factors and coupling strengths (Purcell factor) to a dipolar emitter

Using either quasi-static approximation or exact Mie expansion, we characterize the localized surface plasmons supported by a metallic spherical nanoparticle. We estimate the quality factor $Q_n$ and define the effective volume $V_n$ of the $n^{th}$ mode in a such a way that coupling strength with a neighbouring dipolar emitter is proportional to the ratio $Q_n/V_n$ (Purcell factor). The role of Joule losses, far-field scattering and mode confinement in the coupling mechanism are introduced and discussed with simple physical understanding, with particular attention paid to energy conservation.Comment: (in press) International Journal of Optics (2011

Shocks in dense clouds. IV. Effects of grain-grain processing on molecular line emission

Grain-grain processing has been shown to be an indispensable ingredient of shock modelling in high density environments. For densities higher than \sim10^5 cm-3, shattering becomes a self-enhanced process that imposes severe chemical and dynamical consequences on the shock characteristics. Shattering is accompanied by the vaporization of grains, which can directly release SiO to the gas phase. Given that SiO rotational line radiation is used as a major tracer of shocks in dense clouds, it is crucial to understand the influence of vaporization on SiO line emission. We have developed a recipe for implementing the effects of shattering and vaporization into a 2-fluid shock model, resulting in a reduction of computation time by a factor \sim100 compared to a multi-fluid modelling approach. This implementation was combined with an LVG-based modelling of molecular line radiation transport. Using this model we calculated grids of shock models to explore the consequences of different dust-processing scenarios. Grain-grain processing is shown to have a strong influence on C-type shocks for a broad range of magnetic fields: they become hotter and thinner. The reduction in column density of shocked gas lowers the intensity of molecular lines, at the same time as higher peak temperatures increase the intensity of highly excited transitions compared to shocks without grain-grain processing. For OH the net effect is an increase in line intensities, while for CO and H2O it is the contrary. The intensity of H2 emission is decreased in low transitions and increased for highly excited lines. For all molecules, the highly excited lines become sensitive to the value of the magnetic field. Although vaporization increases the intensity of SiO rotational lines, this effect is weakened by the reduced shock width. The release of SiO early in the hot shock changes the excitation characteristics of SiO radiation.Comment: Published in Astronomy and Astrophysics (2013). 26 pages, 16 figures, 14 table

Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs (Poster Presentation)

Copyright @ 2007 Gu et al; licensee BioMed Central LtdBiochemists often conduct experiments in-vivo in order to explore observable behaviours and understand the dynamics of many intercellular and intracellular processes. However an intuitive understanding of their dynamics is hard to obtain because most pathways of interest involve components connected via interlocking loops. Formal methods for modelling and analysis of biochemical pathways are therefore indispensable. To this end, ODEs (ordinary differential equations) have been widely adopted as a method to model biochemical pathways because they have an unambiguous mathematical format and are amenable to rigorous quantitative analysis. BioNessie http://www.bionessie.com webcite is a workbench for the composition, simulation and analysis of biochemical networks which is being developed in by the Systems Biology team at the Bioinformatics Research Centre as a part of a large DTI funded project 'BPS: A Software Tool for the Simulation and Analysis of Biochemical Networks' http://www.brc.dcs.gla.ac.uk/projects/dti_beacon webcite. BioNessie is written in Java using NetBeans Platform libraries that makes it platform independent. The software employs specialised differential equations solvers for stiff and non-stiff systems to produce model simulation traces. BioNessie provides a user-friendly interfact that comes up with an intuitive tree-based graphical layout, an edition function to SBML-compatible models and feature of data output

Mode-selective quantization and multimodal effective models for spherically layered systems

We propose a geometry-specific, mode-selective quantization scheme in coupled field-emitter systems which makes it easy to include material and geometrical properties, intrinsic losses as well as the positions of an arbitrary number of quantum emitters. The method is presented through the example of a spherically symmetric, non-magnetic, arbitrarily layered system. We follow it up by a framework to project the system on simpler, effective cavity QED models. Maintaining a well-defined connection to the original quantization, we derive the emerging effective quantities from the full, mode-selective model in a mathematically consistent way. We discuss the uses and limitations of these effective models

Nitrogen superfractionation in dense cloud cores

We report new calculations of interstellar 15N fractionation. Previously, we have shown that large enhancements of 15N/14N can occur in cold, dense gas where CO is frozen out, but that the existence of an NH + N channel in the dissociative recombination of N2H+ severely curtails the fractionation. In the light of recent experimental evidence that this channel is in fact negligible, we have reassessed the 15N chemistry in dense cloud cores. We consider the effects of temperatures below 10 K, and of the presence of large amounts of atomic nitrogen. We also show how the temporal evolution of gas-phase isotope ratios is preserved as spatial heterogeneity in ammonia ice mantles, as monolayers deposited at different times have different isotopic compositions. We demonstrate that the upper layers of this ice may have 15N/14N ratios an order of magnitude larger than the underlying elemental value. Converting our ratios to delta-values, we obtain delta(15N) > 3,000 per mil in the uppermost layer, with values as high as 10,000 per mil in some models. We suggest that this material is the precursor to the 15N `hotspots' recently discovered in meteorites and IDPsComment: accepted by MNRA

Individual Entanglements in a Simulated Polymer Melt

We examine entanglements using monomer contacts between pairs of chains in a Brownian-dynamics simulation of a polymer melt. A map of contact positions with respect to the contacting monomer numbers (i,j) shows clustering in small regions of (i,j) which persists in time, as expected for entanglements. Using the ``space''-time correlation function of the aforementioned contacts, we show that a pair of entangled chains exhibits a qualitatively different behavior than a pair of distant chains when brought together. Quantitatively, about 50% of the contacts between entangled chains are persistent contacts not present in independently moving chains. In addition, we account for several observed scaling properties of the contact correlation function.Comment: latex, 12 pages, 7 figures, postscript file available at http://arnold.uchicago.edu/~ebn