The impact of uncertainty in satellite data on the assessment of flood inundation models

The performance of flood inundation models is often assessed using satellite observed data; however these data have inherent uncertainty. In this study we assess the impact of this uncertainty when calibrating a flood inundation model (LISFLOOD-FP) for a flood event in December 2006 on the River Dee, North Wales, UK. The flood extent is delineated from an ERS-2 SAR image of the event using an active contour model (snake), and water levels at the flood margin calculated through intersection of the shoreline vector with LiDAR topographic data. Gauged water levels are used to create a reference water surface slope for comparison with the satellite-derived water levels. Residuals between the satellite observed data points and those from the reference line are spatially clustered into groups of similar values. We show that model calibration achieved using pattern matching of observed and predicted flood extent is negatively influenced by this spatial dependency in the data. By contrast, model calibration using water elevations produces realistic calibrated optimum friction parameters even when spatial dependency is present. To test the impact of removing spatial dependency a new method of evaluating flood inundation model performance is developed by using multiple random subsamples of the water surface elevation data points. By testing for spatial dependency using Moran’s I, multiple subsamples of water elevations that have no significant spatial dependency are selected. The model is then calibrated against these data and the results averaged. This gives a near identical result to calibration using spatially dependent data, but has the advantage of being a statistically robust assessment of model performance in which we can have more confidence. Moreover, by using the variations found in the subsamples of the observed data it is possible to assess the effects of observational uncertainty on the assessment of flooding risk

Helix untwisting and bubble formation in circular DNA

The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path integral techniques, simulates a distribution of topoisomers with various twist numbers and finds the energetically most favorable molecular conformation as a function of temperature. The method can predict helical repeat, openings loci and bubble sizes for specific sequences in a broad temperature range. Some results are presented for a short DNA circle recently identified in mammalian cells.Comment: The Journal of Chemical Physics, vol. 138 (2013), in pres

The pulsar spectral index distribution

The flux density spectra of radio pulsars are known to be steep and, to first order, described by a power-law relationship of the form S_{\nu} \propto \nu^{\alpha}, where S_{\nu} is the flux density at some frequency \nu and \alpha is the spectral index. Although measurements of \alpha have been made over the years for several hundred pulsars, a study of the intrinsic distribution of pulsar spectra has not been carried out. From the result of pulsar surveys carried out at three different radio frequencies, we use population synthesis techniques and a likelihood analysis to deduce what underlying spectral index distribution is required to replicate the results of these surveys. We find that in general the results of the surveys can be modelled by a Gaussian distribution of spectral indices with a mean of -1.4 and unit standard deviation. We also consider the impact of the so-called "Gigahertz-peaked spectrum" pulsars. The fraction of peaked spectrum sources in the population with significant turn-over at low frequencies appears to be at most 10%. We demonstrate that high-frequency (>2 GHz) surveys preferentially select flatter-spectrum pulsars and the converse is true for lower-frequency (<1 GHz) surveys. This implies that any correlations between \alpha and other pulsar parameters (for example age or magnetic field) need to carefully account for selection biases in pulsar surveys. We also expect that many known pulsars which have been detected at high frequencies will have shallow, or positive, spectral indices. The majority of pulsars do not have recorded flux density measurements over a wide frequency range, making it impossible to constrain their spectral shapes. We also suggest that such measurements would allow an improved description of any populations of pulsars with 'non-standard' spectra.Comment: 8 pages, 5 figures. Accepted by MNRA

Optimal conversion of Bose condensed atoms into molecules via a Feshbach resonance

In many experiments involving conversion of quantum degenerate atomic gases into molecular dimers via a Feshbach resonance, an external magnetic field is linearly swept from above the resonance to below resonance. In the adiabatic limit, the fraction of atoms converted into molecules is independent of the functional form of the sweep and is predicted to be 100%. However, for non-adiabatic sweeps through resonance, Landau-Zener theory predicts that a linear sweep will result in a negligible production of molecules. Here we employ a genetic algorithm to determine the functional time dependence of the magnetic field that produces the maximum number of molecules for sweep times that are comparable to the period of resonant atom-molecule oscillations, $2\pi\Omega_{Rabi}^{-1}$. The optimal sweep through resonance indicates that more than 95% of the atoms can be converted into molecules for sweep times as short as $2\pi\Omega_{Rabi}^{-1}$ while the linear sweep results in a conversion of only a few percent. We also find that the qualitative form of the optimal sweep is independent of the strength of the two-body interactions between atoms and molecules and the width of the resonance

An Optimal Dimensionality Multi-shell Sampling Scheme with Accurate and Efficient Transforms for Diffusion MRI

This paper proposes a multi-shell sampling scheme and corresponding transforms for the accurate reconstruction of the diffusion signal in diffusion MRI by expansion in the spherical polar Fourier (SPF) basis. The sampling scheme uses an optimal number of samples, equal to the degrees of freedom of the band-limited diffusion signal in the SPF domain, and allows for computationally efficient reconstruction. We use synthetic data sets to demonstrate that the proposed scheme allows for greater reconstruction accuracy of the diffusion signal than the multi-shell sampling schemes obtained using the generalised electrostatic energy minimisation (gEEM) method used in the Human Connectome Project. We also demonstrate that the proposed sampling scheme allows for increased angular discrimination and improved rotational invariance of reconstruction accuracy than the gEEM schemes.Comment: 4 pages, 4 figures presented at ISBI 201

J-factors of short DNA molecules

The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair fluctuations with respect to the helix diameter are treated as path trajectories in the imaginary time path integral formalism. The partition function for the sub-ensemble of closed molecules is computed by imposing chain ends boundary conditions both on the radial fluctuations and on the angular degrees of freedom. The cyclization probability, the J-factor, proves to be highly sensitive to the stacking potential, mostly to its nonlinear parameters. We find that the J-factor generally decreases by reducing the sequence length ( N ) and, more significantly, below N = 100 base pairs. However, even for very small molecules, the J-factors remain sizeable in line with recent experimental indications. Large bending angles between adjacent base pairs and anharmonic stacking appear as the causes of the helix flexibility at short length scales.Comment: The Journal of Chemical Physics - May 2016 ; 9 page

Multiplicity of fibronectin-binding alpha V integrin receptors in colorectal cancer.

Current data from in vitro and in vivo animal models indicate that fibronectin-binding integrin receptors expressed by colon cancer cells may regulate tumour growth. While individual members of the beta 1 subfamily of integrins have now been clearly identified in colorectal cancer, little information exists with respect to the alpha V subfamily. In the present study we show that alpha V can associate with multiple and different beta subunits capable of binding fibronectin in this tumour type. This is likely to have functional implications for growth and spread of colorectal cancer

Using airborne laser altimetry to improve river flood extents delineated from SAR data

Flood extent maps derived from SAR images are a useful source of data for validating hydraulic models of river flood flow. The accuracy of such maps is reduced by a number of factors, including changes in returns from the water surface caused by different meteorological conditions and the presence of emergent vegetation. The paper describes how improved accuracy can be achieved by modifying an existing flood extent delineation algorithm to use airborne laser altimetry (LiDAR) as well as SAR data. The LiDAR data provide an additional constraint that waterline (land-water boundary) heights should vary smoothly along the flooded reach. The method was tested on a SAR image of a flood for which contemporaneous aerial photography existed, together with LiDAR data of the un-flooded reach. Waterline heights of the SAR flood extent conditioned on both SAR and LiDAR data matched the corresponding heights from the aerial photo waterline significantly more closely than those from the SAR flood extent conditioned only on SAR data

Conformation of Circular DNA in 2 Dimensions

The conformation of circular DNA molecules of various lengths adsorbed in a 2D conformation on a mica surface is studied. The results confirm the conjecture that the critical exponent $\nu$ is topologically invariant and equal to the SAW value (in the present case $\nu=3/4$), and that the topology and dimensionality of the system strongly influences the cross-over between the rigid regime and the self-avoiding regime at a scale $L\approx 8 \ell_p$. Additionally, the bond correlation function scales with the molecular length $L$ as predicted. For molecular lengths $L\leq5 \ell_p$, circular DNA behaves like a stiff molecule with approximately elliptic shape.Comment: 4 pages, 5 figure