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

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

A search for rotating radio transients and fast radio bursts in the Parkes high-latitude pulsar survey

Discoveries of rotating radio transients and fast radio bursts (FRBs) in pulsar surveys suggest that more of such transient sources await discovery in archival data sets. Here we report on a single-pulse search for dispersed radio bursts over a wide range of Galactic latitudes (|b| < $60^{\circ}$) in data previously searched for periodic sources by Burgay et al. We re-detected 20 of the 42 pulsars reported by Burgay et al. and one rotating radio transient reported by Burke-Spolaor. No FRBs were discovered in this survey. Taking into account this result, and other recent surveys at Parkes, we corrected for detection sensitivities based on the search software used in the analyses and the different backends used in these surveys and find that the all-sky FRB event rate for sources with a fluence above 4.0 Jy ms at 1.4 GHz to be ${\cal R} = 4.4^{+5.2}_{-3.1} \times 10^3$ FRBs day$^{-1}$ sky$^{-1}$, where the uncertainties represent a $99\%$ confidence interval. While this rate is lower than inferred from previous studies, as we demonstrate, this combined event rate is consistent with the results of all systematic FRB searches at Parkes to date and does not require the need to postulate a dearth of FRBs at intermediate latitudes.Comment: Accepted, 10 pages, 6 figure

Insight into Resonant Activation in Discrete Systems

The resonant activation phenomenon (RAP) in a discrete system is studied using the master equation formalism. We show that the RAP corresponds to a non-monotonic behavior of the frequency dependent first passage time probability density function (pdf). An analytical expression for the resonant frequency is introduced, which, together with numerical results, helps understand the RAP behavior in the space spanned by the transition rates for the case of reflecting and absorbing boundary conditions. The limited range of system parameters for which the RAP occurs is discussed. We show that a minimum and a maximum in the mean first passage time (MFPT) can be obtained when both boundaries are absorbing. Relationships to some biological systems are suggested.Comment: 5 pages, 5 figures, Phys. Rev. E., in pres

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

SIRT1 Activity Is Linked to Its Brain Region-Specific Phosphorylation and Is Impaired in Huntington’s Disease Mice

Huntingtons disease (HD) is a neurodegenerative disorder for which there are no disease-modifying treatments. SIRT1 is a NAD+-dependent protein deacetylase that is implicated in maintaining neuronal health during development, differentiation and ageing. Previous studies suggested that the modulation of SIRT1 activity is neuroprotective in HD mouse models, however, the mechanisms controlling SIRT1 activity are unknown. We have identified a striatum-specific phosphorylation-dependent regulatory mechanism of SIRT1 induction under normal physiological conditions, which is impaired in HD. We demonstrate that SIRT1 activity is down-regulated in the brains of two complementary HD mouse models, which correlated with altered SIRT1 phosphorylation levels. This SIRT1 impairment could not be rescued by the ablation of DBC1, a negative regulator of SIRT1, but was linked to changes in the sub-cellular distribution of AMPK-α1, a positive regulator of SIRT1 function. This work provides insights into the regulation of SIRT1 activity with the potential for the development of novel therapeutic strategies

Radiation Induced Damage in GaAs Particle Detectors

The motivation for investigating the use of GaAs as a material for detecting particles in experiments for High Energy Physics (HEP) arose from its perceived resistance to radiation damage. This is a vital requirement for detector materials that are to be used in experiments at future accelerators where the radiation environments would exclude all but the most radiation resistant of detector types.Comment: 5 pages. PS file only - original in WORD Also available at http://ppewww.ph.gla.ac.uk/preprints/97/06