An alternative approach to the solution of a class of Wiener-Hopf and related problems Technical report no. 8

Alternative method to Weiner-Hopf approach for solving radiation and diffraction problem

A technique for solving certain Wiener-Hopf type boundary value problems Technical report no. 9

Technique for solving Weiner-Hopf type boundary value problem

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

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

Validation of a model of regulation in the tryptophan operon against multiple experiment data using global optimisation

This paper is concerned with validating a mathematical model of regulation in the tryptophan operon using global optimization. Although a number of models for this biochemical network are proposed, in many cases only qualitative agreement between the model output and experimental data was demonstrated, since very little information is currently available to guide the selection of parameter values for the models. This paper presents a model validating method using both multiple experimental data and global optimization

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

Principle of scaling in a uniaxial medium scientific report no. 6

Solution to Maxwell equations for source currents in unbounded magnetoionic medium for which dielectric tensor is uniaxia