An Optimal Dimensionality Sampling Scheme on the Sphere for Antipodal Signals In Diffusion Magnetic Resonance Imaging

We propose a sampling scheme on the sphere and develop a corresponding spherical harmonic transform (SHT) for the accurate reconstruction of the diffusion signal in diffusion magnetic resonance imaging (dMRI). By exploiting the antipodal symmetry, we design a sampling scheme that requires the optimal number of samples on the sphere, equal to the degrees of freedom required to represent the antipodally symmetric band-limited diffusion signal in the spectral (spherical harmonic) domain. Compared with existing sampling schemes on the sphere that allow for the accurate reconstruction of the diffusion signal, the proposed sampling scheme reduces the number of samples required by a factor of two or more. We analyse the numerical accuracy of the proposed SHT and show through experiments that the proposed sampling allows for the accurate and rotationally invariant computation of the SHT to near machine precision accuracy.Comment: Will be published in the proceedings of the International Conference Acoustics, Speech and Signal Processing 2015 (ICASSP'2015

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

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

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

Emergence of steady and oscillatory localized structures in a phytoplankton-nutrient model

Co-limitation of marine phytoplankton growth by light and nutrient, both of which are essential for phytoplankton, leads to complex dynamic behavior and a wide array of coherent patterns. The building blocks of this array can be considered to be deep chlorophyll maxima, or DCMs, which are structures localized in a finite depth interior to the water column. From an ecological point of view, DCMs are evocative of a balance between the inflow of light from the water surface and of nutrients from the sediment. From a (linear) bifurcational point of view, they appear through a transcritical bifurcation in which the trivial, no-plankton steady state is destabilized. This article is devoted to the analytic investigation of the weakly nonlinear dynamics of these DCM patterns, and it has two overarching themes. The first of these concerns the fate of the destabilizing stationary DCM mode beyond the center manifold regime. Exploiting the natural singularly perturbed nature of the model, we derive an explicit reduced model of asymptotically high dimension which fully captures these dynamics. Our subsequent and fully detailed study of this model - which involves a subtle asymptotic analysis necessarily transgressing the boundaries of a local center manifold reduction - establishes that a stable DCM pattern indeed appears from a transcritical bifurcation. However, we also deduce that asymptotically close to the original destabilization, the DCM looses its stability in a secondary bifurcation of Hopf type. This is in agreement with indications from numerical simulations available in the literature. Employing the same methods, we also identify a much larger DCM pattern. The development of the method underpinning this work - which, we expect, shall prove useful for a larger class of models - forms the second theme of this article

A finite element based formulation for sensitivity studies of piezoelectric systems

Sensitivity Analysis is a branch of numerical analysis which aims to quantify the affects that variability in the parameters of a numerical model have on the model output. A finite element based sensitivity analysis formulation for piezoelectric media is developed here and implemented to simulate the operational and sensitivity characteristics of a piezoelectric based distributed mode actuator (DMA). The work acts as a starting point for robustness analysis in the DMA technology

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

Probing a non-biaxial behavior of infinitely thin hard platelets

We give a criterion to test a non-biaxial behavior of infinitely thin hard platelets of $D_{2h}$ symmetry based upon the components of three order parameter tensors. We investigated the nematic behavior of monodisperse infinitely thin rectangular hard platelet systems by using the criterion. Starting with a square platelet system, and we compared it with rectangular platelet systems of various aspect ratios. For each system, we performed equilibration runs by using isobaric Monte Carlo simulations. Each system did not show a biaxial nematic behavior but a uniaxial nematic one, despite of the shape anisotropy of those platelets. The relationship between effective diameters by simulations and theoretical effective diameters of the above systems was also determined.Comment: Submitted to JPS

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