Thesis (M.Ing. (Nuclear Engineering))--North-West University, Potchefstroom Campus, 2008.

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Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.

Corrosion of reinforcing bars is the major cause of deterioration of reinforced concrete (RC) structures in North America, Europe, the Middle East, and many coastal regions around the world. This deterioration leads to a loss of serviceability and functionality and ultimately affects the structural safety. The objective of this research is to formulate and implement a general stochastic finite element analysis (SFEA) framework for the time-dependent reliability analysis of RC beams with corroding flexural reinforcement. The framework is based on the integration of nonlinear finite element and reliability analyses through an iterative response surface methodology (RSM). Corrosion-induced damage is modelled through the combined effects of gradual loss of the cross-sectional area of the steel reinforcement and the reduction bond between steel and concrete for increasing levels of corrosion. Uncertainties in corrosion rate, material properties, and imposed actions are modelled as random variables. Effective implementation of the framework is achieved by the coupling of commercial finite element and reliability software. Application of the software is demonstrated through a case study of a simply-supported RC girder with tension reinforcement subjected to the effects of uniform (general) corrosion, in which two limit states are considered: (i) a deflection serviceability limit state and (ii) flexural strength ultimate limit state. The results of the case study show that general corrosion leads to a very significant decrease in the reliability of the RC beam both in terms of flexural strength and maximum deflections. The loss of strength and serviceability was shown to be predominantly caused by the loss of bond strength, whereas the gradual reduction of the cross-sectional area of tension reinforcement was found to be insignificant. The load-deflection response is also significantly affected by the deterioration of bond strength (flexural strength and stiffness). The probability of failure at the end of service life, due to the effects of uniform corrosion-induced degradation, is observed to be approximately an order of magnitude higher than in the absence of corrosion. Furthermore, the results suggest that flexural resistance of corroded RC beams is controlled by the anchorage (bond) of the bars and not by the yielding of fully bonded tensile reinforcement at failure. This is significant since the end regions can be severely corroded due to chloride, moisture, and oxygen access at connections and expansion joints. The research strongly suggests that bond damage must be considered in the assessment of the time-dependent reliability of RC beams subjected to general corrosion.

This thesis presents the Differential Quadrature Method (DQM) for solving time-dependent or heat conduction problem. DQM discretizes the space derivatives giving a system of ordinary differential equations with respect to time and the fourth order Runge Kutta Method (RKM) is employed for solving this system. Stabilities of the ordinary differential equations system and RKM are considered and step sizes are arranged accordingly. The procedure is applied to several time dependent diffusion problems and the solutions are presented in terms of graphics comparing with the exact solutions. This method exhibits high accuracy and efficiency comparing to the other numerical methods.

A general finite difference discretization of the time-dependent radiation transport equation is developed around the framework of an existing steady-state three dimensional radiation transport solver based on the slice-balance approach. Three related algorithms are outlined within the general finite difference scheme: an explicit, an implicit, and a semi-implicit approach. The three algorithms are analyzed with respect to the discretizations of each element of the phase space in the transport solver. The explicit method, despite its small computational cost per time step, is found to be unsuitable for many purposes due to its inability to accurately handle rapidly varying solutions. The semi-implicit method is shown to produce results nearly as reliable as the fully implicit solver, while requiring significantly less computational effort.

The kicked-rotor under the Aharonov-Bohm effect are studyed by using the floquet map, the energy change with different magnetic flux have also being discussed. Finally, the kicked-rotor under the time-dependent magnetic flux are discussed.

Sandwich beams are composite systems having high stiffness-to-weight and strength-to-weight ratios and are used as light weight load bearing components. The use of thin, strong skin sheets adhered to thicker, lightweight core materials has allowed industry to build strong, stiff, light, and durable structures. Due to the use of viscoelastic polymer constituents, sandwich beams can exhibit time-dependent behavior. This study examines and predicts the time-dependent behavior of sandwich beams driven by the viscoelastic foam core. Governing equations of the deformation of viscoelastic materials are often represented in differential form or hereditary integral form. A single integral constitutive equation is used to model linear viscoelastic materials by means of the Boltzmann superposition principle. Based on the strength of materials approach, the analytical solution for the deformation in a viscoelastic sandwich beam is determined based on the application of the Correspondence Principle and Laplace transform. Finite element (FE) method is used to analyze the overall transient responses of the sandwich systems subject to a concentrated point load at the midspan of the beam. A 2D plane strain element is used to generate meshes of the three-point bending beam. User material (UMAT) subroutine in ABAQUS FE code is utilized to incorporate the viscoelastic constitutive model for the foam core. Analytical models and experimental data available in the literature are used to verify the results obtained from the FE analysis. The stress, strain, and deformation fields during creep responses are analyzed. Parameters such as the viscosity of the foam core, the ratio of the skin and core thicknesses, the ratio of the skin and core moduli, and adhesive layers are varied and their effect on the timedependent behavior of the sandwich system is examined.

In this thesis, the two-dimensional initial and boundary value problems governed by unsteady partial differential equations are solved by making use of boundary element techniques. The boundary element method (BEM) with time-dependent fundamental solution is presented as an efficient procedure for the solution of diffusion, wave and convection-diffusion equations. It interpenetrates the equations in such a way that the boundary solution is advanced to all time levels, simultaneously. The solution at a required interior point can then be obtained by using the computed boundary solution. Then, the coupled system of nonlinear reaction-diffusion equations and the magnetohydrodynamic (MHD) flow equations in a duct are solved by using the time-domain BEM. The numerical approach is based on the iteration between the equations of the system. The advantage of time-domain BEM are still made use of utilizing large time increments. Mainly, MHD flow equations in a duct having variable wall conductivities are solved successfully for large values of Hartmann number. Variable conductivity on the walls produces coupled boundary conditions which causes difficulties in numerical treatment of the problem by the usual BEM. Thus, a new time-domain BEM approach is derived in order to solve these equations as a whole despite the coupled boundary conditions, which is one of the main contributions of this thesis. Further, the full MHD equations in stream function-vorticity-magnetic induction-current density form are solved. The dual reciprocity boundary element method (DRBEM), producing only boundary integrals, is used due to the nonlinear convection terms in the equations. In addition, the missing boundary conditions for vorticity and current density are derived with the help of coordinate functions in DRBEM. The resulting ordinary differential equations are discretized in time by using unconditionally stable Gear&#039 / s scheme so that large time increments can be used. The Navier-Stokes equations are solved in a square cavity up to Reynolds number 2000. Then, the solution of full MHD flow in a lid-driven cavity and a backward facing step is obtained for different values of Reynolds, magnetic Reynolds and Hartmann numbers. The solution procedure is quite efficient to capture the well known characteristics of MHD flow.

The electron transport through a molecular wire under the influence of an external laser field is studied using a reduced density matrix formalism. The full system is partitioned into the relevant part, i.e. the wire, electron reservoirs and a phonon bath. An earlier second-order perturbation theory approach of Meier and Tannor for bosonic environments which employs a numerical decomposition of the spectral density is used to describe the coupling to the phonon bath and is extended to deal with the electron transfer between the reservoirs and the molecular wire. Furthermore, from the resulting time-nonlocal (TNL) scheme a time-local (TL) approach can be determined. Both are employed to propagate the reduced density operator in time for an arbitrary time-dependent system Hamiltonian which incorporates the laser field non-perturbatively. Within the TL formulation, one can extract a current operator for the open quantum system. This enables a more general formulation of the problem which is necessary to employ an optimal control algorithm for open quantum systems in order to compute optimal control fields for time-distributed target states, e.g. current patterns. Thus, we take a fundamental step towards optimal control in molecular electronics. Numerical examples of the population dynamics, laser controlled current, TNL vs. TL and optimal control fields are presented to demonstrate the diverse applicability of the derived formalism.