An investigation into approximate solutions for deterministic and stochastic multi-dimensional sequencing

A description is given of an investigation in detail into the validity of the overlap integral method for describing planar optical waveguide junctions. A comparison between the results of this method and that of a rigorous mode-matching approach is taken

Crossover from magnetostatic to exchange coupling in La0.67Ca0.33MnO3/YBa2Cu3O7/La0.67Ca0.33MnO3 heterostructures

The influence of YBa2Cu3O4 (YBCO) superconductor layer (S-layer) with varying thickness d-YBCO = 20 to 50 nm on the magnetic coupling between two La0.67Ca0.33MnO3 (LCMO) ferromagnet layers (F-layer, thickness d-LCMO = 50 nm) in F/S/F heterostructures (HSs) was investigated by measuring global magnetization (M) in a temperature (T) range = 2 - 300 K and magnetic field (H) range = 0 - 10 kOe. All the HSs were superconducting with critical temperature (Tc) decreasing from = 78 to 36 K with decrease in d-YBCO, whereas the ferromagnetic ordering temperature Tm = 250 K did not change much. Systematically measured M-H loops of all HSs at both T > Tc and T < Tc show three main results- (a) the two step magnetic reversal above Tc converts into a four step reversal below Tc in HSs with d-YBCO >= 30 nm, (b) the magnetic field corresponding to the additional two switching steps and their magnitude show characteristic evolution with T and d-YBCO and (c) the HS with d-YBCO = 20 nm shows radically different behaviour, where the two step magnetic reversal above Tc continues to persist below Tc and converts into a single step reversal at T << Tc. The first two results indicate magnetostatic coupling between the magnetic domains and the vortices across the two F/S interfaces resulting in reversal dynamics different from that deep within the LCMO layers. Whereas, the result c reveals indirect exchange coupling between LCMO layers through the superconducting YBCO layer, which is a clear experimental evidence of coexistence of ferromagnetism and superconductivity in nm scale F/S/F HSs expected theoretically by C.A.R. Sa de Melo (Physica C 387, 17-25 (2003)).Comment: 23 pages, 7 figures, accepted in JPC

Effects of Nanodots Shape and Lattice Constants on the Spin Wave Dynamics of Patterned Permalloy Dots

Micromagnetic simulations studies on Permalloy (Ni80Fe20) nanodot with different shape and edge-to-edge separation (s) down to 25nm arranged in square lattice are reported. We observe the significant variation of spin-wave (SW) dynamics of nanodots of different shapes (triangular, diamond and hexagon) and of fixed dot diameter 100nm with varying s. Modes for single dot are transformed in an array into multiple quantized, edge and centre modes for different shapes and edge-to-edge separations, with different spin wave frequencies and peak intensities. Specifically, in the triangular dot sample, a broad range of mode frequencies is observed with highest SW frequency 14.7 GHz. For separation less than 100nm, the SW frequencies undergoes significant modification due to the varying nature of the magnetostatic and dipolar interaction in the array while for separation above 100nm, the SW frequency mostly remain constant. The power profiles confirm the nature of the observed modes. The spatial profiles of magnetostatic field are determined by a combination of internal magnetic-field profiles within the nanodots and the magnetostatic fields within the lattice. The inter-dots interaction of magnetostatic field shows dipolar and quadrupole contributions for all the shapes. Interestingly, vortex states with shifted core and polarity are observed in the array for all the shapes at Hbias = 0. Our results provide important understanding about the tunability of SW spectra in the array of triangular, diamond and hexagon shaped nanoelements.Comment: 13 pages, 8 figure

Epigenetic modelling: DNA methylation and working towards model parameterisation

The main focus of the research in this thesis is the investigation in DNA methylation mechanisms of epigenetics and the study of a specific database. As part of the latter work, the role of curation is described, and a new knowledge management system, PathEpigen1 , is reported that is currently being developed for colon cancer in the Sci-Sym centre. The database deals with genetic and epigenetic interactions and contains considerable data on molecular events such as genetic and epigenetic events. The data curation includes biomedical and biological information. An efficient method was devised to extract biological information from the literature to process, manage and upgrade data. We present a Deterministic Finite Automata (DFA) model for the DNA methylation mechanism controlled by DNA methyltransferase (DNMT) enzymes. This thesis provides a brief introduction to epigenetics, a survey of ongoing research on computational epigenetics and a description of the DNA methylation database. Furthermore, it also gives an overview of DNA methylation and its importance in cancer. The DFA models three states of methylation frequency (normal, de-novo and hypermethylated) in the cell. It has been executed on input of random strings of size 100. Out of the strings considered, we found that 26%, 37% and 37% correspond to normal, de-novo (cancer initiation) and hypermethylated (cancer) states, respectively