19,527 research outputs found

    Helix untwisting and bubble formation in circular DNA

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    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

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

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    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, 2πΩRabi−12\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 2πΩRabi−12\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

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    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

    Thick silicon growth techniques

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    Hall mobility measurements on a number of single crystal silicon ribbons grown from graphite dies have shown some ribbons to have mobilities consistent with their resistivities. The behavior of other ribbons appears to be explained by the introduction of impurities of the opposite sign. Growth of a small single crystal silicon ribbon has been achieved from a beryllia dia. Residual internal stresses of the order of 7 to 18,000 psi have been determined to exist in some silicon ribbon, particularly those grown at rates in excess of 1 in./min. Growth experiments have continued toward definition of a configuration and parameters to provide a reasonable yield of single crystal ribbons. High vacuum outgassing of graphite dies and evacuation and backfilling of growth chambers have provided significant improvements in surface quality of ribbons grown from graphite dies

    How to Avoid Common Pitfalls of Health IT Implementation

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    The stories in this guide were based on case studies about a specific intensive care IT system that integrates information from bedside monitors into a single intuitive display to provide better real-time information for clinicians

    J-factors of short DNA molecules

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    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

    C*-algebras of labelled graphs II - Simplicity results

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    We prove simplicity and pure infiniteness results for a certain class of labelled graph C∗C^*-algebras. We show, by example, that this class of unital labelled graph C∗C^*-algebras is strictly larger than the class of unital graph C∗C^*-algebras.Comment: 18 pages, 4 figure
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