Optical tweezers using highly focussed laser beams can be used to exert forces and torques and thus drive micromachines. This opens up a new field of microengineering, whose potential has yet to be fully realized. Until now, methods that have been used for modelling optical tweezers are limited to scatterers that are homogeneous or that have simple geometry. To aid in designing more general micromachines, I developed and implemented two main methods for modelling the micromachines that we use. These methods can be used for further proposed structures to be fabricated. The first is a FDFD/T-matrix hybrid method that incorporates the finite difference frequency domain (FDFD) method, which is used for inhomogeneous and anisotropic media, with vector spherical wave functions (VSWF) to formulate the T-matrix. The T-matrix is then used to calculate the torque of the trapped vaterite sphere, which is apparently composed of birefringent unit crystals but the bulk structure appears to be arranged in a sheaf-of-wheat fashion. The second method is formulating the T-matrix via discrete dipole approximation (DDA) of complex arbitrarily shaped mesoscale objects and implementing symmetry optimizations to allow calculations to be performed on high-end desktop PCs that are otherwise impractical due to memory requirements and calculation time. This method was applied to modelling microrotors. The T-matrix represents the scattering properties of an object for a given wavelength. Once it is calculated, subsequent calculations with different illumination conditions can be performed rapidly. This thesis also deals with studies of other light scattering phenomena including the modelling of scattered fields from protein molecules subsequently used to model FRET resonance, determining the limits of trappability, interferometric Brownian motion and the comparison between integral transforms by direct numerical integration and overdetermined point-matching.

Quantum entanglement is widely renounced as one of the most fundamental concepts of quantum mechanics. Such phenomenon exhibit non-local interaction properties which cannot be explained classically. In this thesis, we address a number of problems associated with creating, transferring and engineering of entanglement between two separate parties. The work is motivated by a desire to better understand the dynamics of entanglement between systems. In particular, the research is mainly focused on the study of the dynamics of the well known maximally entangled Bell state under different influences such as decoherence and inter-qubit coupling. We show the connection between coherence and entanglement using the system sub jected to decoherence. We also confirm the transfer of entanglement between completely isolated partite using the double Jaynes-Cummings model. Based on this result, we propose a new conservation criterion proven to be general for single excitation systems. Such conservation criterion are then compared and extended to a general N qubit systems. In addition, an attempt is made to evaluate entanglement conservation rules for the EPR- like multipartite entanglement. We also describe a new technique for solving entanglement in the top-down way ignoring physical setup.

Quantum entanglement is widely renounced as one of the most fundamental concepts of quantum mechanics. Such phenomenon exhibit non-local interaction properties which cannot be explained classically. In this thesis, we address a number of problems associated with creating, transferring and engineering of entanglement between two separate parties. The work is motivated by a desire to better understand the dynamics of entanglement between systems. In particular, the research is mainly focused on the study of the dynamics of the well known maximally entangled Bell state under different influences such as decoherence and inter-qubit coupling. We show the connection between coherence and entanglement using the system sub jected to decoherence. We also confirm the transfer of entanglement between completely isolated partite using the double Jaynes-Cummings model. Based on this result, we propose a new conservation criterion proven to be general for single excitation systems. Such conservation criterion are then compared and extended to a general N qubit systems. In addition, an attempt is made to evaluate entanglement conservation rules for the EPR- like multipartite entanglement. We also describe a new technique for solving entanglement in the top-down way ignoring physical setup.

Optical tweezers using highly focussed laser beams can be used to exert forces and torques and thus drive micromachines. This opens up a new field of microengineering, whose potential has yet to be fully realized. Until now, methods that have been used for modelling optical tweezers are limited to scatterers that are homogeneous or that have simple geometry. To aid in designing more general micromachines, I developed and implemented two main methods for modelling the micromachines that we use. These methods can be used for further proposed structures to be fabricated. The first is a FDFD/T-matrix hybrid method that incorporates the finite difference frequency domain (FDFD) method, which is used for inhomogeneous and anisotropic media, with vector spherical wave functions (VSWF) to formulate the T-matrix. The T-matrix is then used to calculate the torque of the trapped vaterite sphere, which is apparently composed of birefringent unit crystals but the bulk structure appears to be arranged in a sheaf-of-wheat fashion. The second method is formulating the T-matrix via discrete dipole approximation (DDA) of complex arbitrarily shaped mesoscale objects and implementing symmetry optimizations to allow calculations to be performed on high-end desktop PCs that are otherwise impractical due to memory requirements and calculation time. This method was applied to modelling microrotors. The T-matrix represents the scattering properties of an object for a given wavelength. Once it is calculated, subsequent calculations with different illumination conditions can be performed rapidly. This thesis also deals with studies of other light scattering phenomena including the modelling of scattered fields from protein molecules subsequently used to model FRET resonance, determining the limits of trappability, interferometric Brownian motion and the comparison between integral transforms by direct numerical integration and overdetermined point-matching.

Quantum entanglement is widely renounced as one of the most fundamental concepts of quantum mechanics. Such phenomenon exhibit non-local interaction properties which cannot be explained classically. In this thesis, we address a number of problems associated with creating, transferring and engineering of entanglement between two separate parties. The work is motivated by a desire to better understand the dynamics of entanglement between systems. In particular, the research is mainly focused on the study of the dynamics of the well known maximally entangled Bell state under different influences such as decoherence and inter-qubit coupling. We show the connection between coherence and entanglement using the system sub jected to decoherence. We also confirm the transfer of entanglement between completely isolated partite using the double Jaynes-Cummings model. Based on this result, we propose a new conservation criterion proven to be general for single excitation systems. Such conservation criterion are then compared and extended to a general N qubit systems. In addition, an attempt is made to evaluate entanglement conservation rules for the EPR- like multipartite entanglement. We also describe a new technique for solving entanglement in the top-down way ignoring physical setup.

Monte Carlo simulation methods are becoming increasingly important for solving difficult optimization problems. Monte Carlo methods are often used when it is infeasible to determine an exact result via a deterministic algorithm, such as with NP or #P problems. Several recent Monte Carlo techniques employ the idea of importance sampling; examples include the Cross-Entropy method and sequential importance sampling. The Cross-Entropy method is a relatively new Monte Carlo technique that has been successfully applied to a wide range of optimization and estimation problems since introduced by R. Y. Rubinstein in 1997. However, as the problem size increases, the Cross-Entropy method, like many heuristics, can take an exponentially increasing amount of time before it returns a solution. For large problems this can lead to an impractical amount of running time. A main aim of this thesis is to develop the Cross-Entropy method for large-scale parallel computing, allowing the running time of a Cross-Entropy program to be significantly reduced by the use of additional computing resources. The effectiveness of the parallel approach is demonstrated via a number of numerical studies. A second aim is to apply the Cross-Entropy method and sequential importance sampling to biological problems, in particular the multiple change-point problem for DNA sequences. The multiple change-point problem in a general setting is the problem of identifying, given a particular sequence of numbers/characters, a point along that sequence where some property of interest changes abruptly. An example in a biological setting, is identifying points in a DNA sequence where there is a significant change in the proportion of the nucleotides G and C with respect to the nucleotides A and T. We show that both sequential importance sampling and the Cross-Entropy approach yield significant improvements in time and/or accuracy over existing techniques.

Consider distinct latin squares, L and M, of order n. Then the pair (T1, T2) where T1 = L \M and T2 = M \ L is called a latin bitrade. Furthermore T1 and T2 are referred to as latin trades, in which T2 is said to be a disjoint mate of T1 (and vice versa). Drápal (1991) showed that, under certain conditions, a partition of an equilateral triangle of side length n, where n is some integer, into smaller, integer length sided equilateral triangles gives rise to a latin trade within the latin square based on the addition table for the integers modulo n. A partial latin square P of order n is said to be completable if there exists a latin square L of order n such that P ⊆ L. If there is only one such possible latin square, L, of order n then P is said to be uniquely completable and P is called a defining set of L. Furthermore, if C is a uniquely completable partial latin square such that no proper subset of C is uniquely completable, C is said to be a critical set or a minimal defining set. These concepts, namely latin trades and defining sets in latin squares, are intimately connected by the following observation. If L is a latin square and D ⊆ L is a defining set, then D intersects all latin bitrades for which one mate is contained in L. In Part I of this thesis Dr´apal’s result is applied to investigate the structure of certain defining sets in latin squares. The results that are obtained are interesting in themselves; furthermore, the geometric approach to the problem yields additional appealing results. These geometric results are discussed in Chapters 3, 4, 5 and 6. They pertain to partitioning regions (polygons in R2 that satisfy certain obvious conditions) into equilateral, integer length sided, triangles, such that no point, in the region, is a corner of more than three distinct triangles. In Chapter 2 one of the main two theorems on defining sets is established, as is a method for using the above geometric results to prove the nonexistence of certain types of defining sets. In Part II of this thesis, intersection problems, for latin squares and Steiner triple systems, are considered. The seminal works, for problems of these types, are due to Lindner and Rosa (1975) and Fu (1980). A natural progression, from the established literature, for intersection problems between elements in a pair of latin squares or Steiner triple systems is to problems in which the intersection is composed of a number of disjoint configurations (isomorphic copies of some specified partial triple system). In this thesis solutions to two intersection problems for disjoint configurations are detailed. An m-flower, (F,F), is a partial triple system/configuration, such that: F = {{x, yi, zi} | {yi, zi} ∩ {yj , zj} = ∅, for 0 ≤ i, j ≤ m − 1, i 6= j}; and F = UX∈FX. The first such problem considered in this thesis asks for necessary and sufficient conditions for integers k and m ≥ 2 such that a pair of latin squares of order n exists that intersect precisely in k disjoint m-flowers. The necessary terminology, constructions, lemmas and proof for this result are contained in Chapters 7, 8 and 9. The second such problem considered in this thesis asks for necessary and sufficient conditions for integers k such that a pair of Steiner triple systems of order u exists that intersect precisely in k disjoint 2-flowers. This result relies on the solution to the latin square problem and an additional result from Chapter 9. The further constructions and lemmas used to prove this result are detailed in Chapter 10.

Consider distinct latin squares, L and M, of order n. Then the pair (T1, T2) where T1 = L \M and T2 = M \ L is called a latin bitrade. Furthermore T1 and T2 are referred to as latin trades, in which T2 is said to be a disjoint mate of T1 (and vice versa). Drápal (1991) showed that, under certain conditions, a partition of an equilateral triangle of side length n, where n is some integer, into smaller, integer length sided equilateral triangles gives rise to a latin trade within the latin square based on the addition table for the integers modulo n. A partial latin square P of order n is said to be completable if there exists a latin square L of order n such that P ⊆ L. If there is only one such possible latin square, L, of order n then P is said to be uniquely completable and P is called a defining set of L. Furthermore, if C is a uniquely completable partial latin square such that no proper subset of C is uniquely completable, C is said to be a critical set or a minimal defining set. These concepts, namely latin trades and defining sets in latin squares, are intimately connected by the following observation. If L is a latin square and D ⊆ L is a defining set, then D intersects all latin bitrades for which one mate is contained in L. In Part I of this thesis Dr´apal’s result is applied to investigate the structure of certain defining sets in latin squares. The results that are obtained are interesting in themselves; furthermore, the geometric approach to the problem yields additional appealing results. These geometric results are discussed in Chapters 3, 4, 5 and 6. They pertain to partitioning regions (polygons in R2 that satisfy certain obvious conditions) into equilateral, integer length sided, triangles, such that no point, in the region, is a corner of more than three distinct triangles. In Chapter 2 one of the main two theorems on defining sets is established, as is a method for using the above geometric results to prove the nonexistence of certain types of defining sets. In Part II of this thesis, intersection problems, for latin squares and Steiner triple systems, are considered. The seminal works, for problems of these types, are due to Lindner and Rosa (1975) and Fu (1980). A natural progression, from the established literature, for intersection problems between elements in a pair of latin squares or Steiner triple systems is to problems in which the intersection is composed of a number of disjoint configurations (isomorphic copies of some specified partial triple system). In this thesis solutions to two intersection problems for disjoint configurations are detailed. An m-flower, (F,F), is a partial triple system/configuration, such that: F = {{x, yi, zi} | {yi, zi} ∩ {yj , zj} = ∅, for 0 ≤ i, j ≤ m − 1, i 6= j}; and F = UX∈FX. The first such problem considered in this thesis asks for necessary and sufficient conditions for integers k and m ≥ 2 such that a pair of latin squares of order n exists that intersect precisely in k disjoint m-flowers. The necessary terminology, constructions, lemmas and proof for this result are contained in Chapters 7, 8 and 9. The second such problem considered in this thesis asks for necessary and sufficient conditions for integers k such that a pair of Steiner triple systems of order u exists that intersect precisely in k disjoint 2-flowers. This result relies on the solution to the latin square problem and an additional result from Chapter 9. The further constructions and lemmas used to prove this result are detailed in Chapter 10.

Consider distinct latin squares, L and M, of order n. Then the pair (T1, T2) where T1 = L \M and T2 = M \ L is called a latin bitrade. Furthermore T1 and T2 are referred to as latin trades, in which T2 is said to be a disjoint mate of T1 (and vice versa). Drápal (1991) showed that, under certain conditions, a partition of an equilateral triangle of side length n, where n is some integer, into smaller, integer length sided equilateral triangles gives rise to a latin trade within the latin square based on the addition table for the integers modulo n. A partial latin square P of order n is said to be completable if there exists a latin square L of order n such that P ⊆ L. If there is only one such possible latin square, L, of order n then P is said to be uniquely completable and P is called a defining set of L. Furthermore, if C is a uniquely completable partial latin square such that no proper subset of C is uniquely completable, C is said to be a critical set or a minimal defining set. These concepts, namely latin trades and defining sets in latin squares, are intimately connected by the following observation. If L is a latin square and D ⊆ L is a defining set, then D intersects all latin bitrades for which one mate is contained in L. In Part I of this thesis Dr´apal’s result is applied to investigate the structure of certain defining sets in latin squares. The results that are obtained are interesting in themselves; furthermore, the geometric approach to the problem yields additional appealing results. These geometric results are discussed in Chapters 3, 4, 5 and 6. They pertain to partitioning regions (polygons in R2 that satisfy certain obvious conditions) into equilateral, integer length sided, triangles, such that no point, in the region, is a corner of more than three distinct triangles. In Chapter 2 one of the main two theorems on defining sets is established, as is a method for using the above geometric results to prove the nonexistence of certain types of defining sets. In Part II of this thesis, intersection problems, for latin squares and Steiner triple systems, are considered. The seminal works, for problems of these types, are due to Lindner and Rosa (1975) and Fu (1980). A natural progression, from the established literature, for intersection problems between elements in a pair of latin squares or Steiner triple systems is to problems in which the intersection is composed of a number of disjoint configurations (isomorphic copies of some specified partial triple system). In this thesis solutions to two intersection problems for disjoint configurations are detailed. An m-flower, (F,F), is a partial triple system/configuration, such that: F = {{x, yi, zi} | {yi, zi} ∩ {yj , zj} = ∅, for 0 ≤ i, j ≤ m − 1, i 6= j}; and F = UX∈FX. The first such problem considered in this thesis asks for necessary and sufficient conditions for integers k and m ≥ 2 such that a pair of latin squares of order n exists that intersect precisely in k disjoint m-flowers. The necessary terminology, constructions, lemmas and proof for this result are contained in Chapters 7, 8 and 9. The second such problem considered in this thesis asks for necessary and sufficient conditions for integers k such that a pair of Steiner triple systems of order u exists that intersect precisely in k disjoint 2-flowers. This result relies on the solution to the latin square problem and an additional result from Chapter 9. The further constructions and lemmas used to prove this result are detailed in Chapter 10.

Consider distinct latin squares, L and M, of order n. Then the pair (T1, T2) where T1 = L \M and T2 = M \ L is called a latin bitrade. Furthermore T1 and T2 are referred to as latin trades, in which T2 is said to be a disjoint mate of T1 (and vice versa). Drápal (1991) showed that, under certain conditions, a partition of an equilateral triangle of side length n, where n is some integer, into smaller, integer length sided equilateral triangles gives rise to a latin trade within the latin square based on the addition table for the integers modulo n. A partial latin square P of order n is said to be completable if there exists a latin square L of order n such that P ⊆ L. If there is only one such possible latin square, L, of order n then P is said to be uniquely completable and P is called a defining set of L. Furthermore, if C is a uniquely completable partial latin square such that no proper subset of C is uniquely completable, C is said to be a critical set or a minimal defining set. These concepts, namely latin trades and defining sets in latin squares, are intimately connected by the following observation. If L is a latin square and D ⊆ L is a defining set, then D intersects all latin bitrades for which one mate is contained in L. In Part I of this thesis Dr´apal’s result is applied to investigate the structure of certain defining sets in latin squares. The results that are obtained are interesting in themselves; furthermore, the geometric approach to the problem yields additional appealing results. These geometric results are discussed in Chapters 3, 4, 5 and 6. They pertain to partitioning regions (polygons in R2 that satisfy certain obvious conditions) into equilateral, integer length sided, triangles, such that no point, in the region, is a corner of more than three distinct triangles. In Chapter 2 one of the main two theorems on defining sets is established, as is a method for using the above geometric results to prove the nonexistence of certain types of defining sets. In Part II of this thesis, intersection problems, for latin squares and Steiner triple systems, are considered. The seminal works, for problems of these types, are due to Lindner and Rosa (1975) and Fu (1980). A natural progression, from the established literature, for intersection problems between elements in a pair of latin squares or Steiner triple systems is to problems in which the intersection is composed of a number of disjoint configurations (isomorphic copies of some specified partial triple system). In this thesis solutions to two intersection problems for disjoint configurations are detailed. An m-flower, (F,F), is a partial triple system/configuration, such that: F = {{x, yi, zi} | {yi, zi} ∩ {yj , zj} = ∅, for 0 ≤ i, j ≤ m − 1, i 6= j}; and F = UX∈FX. The first such problem considered in this thesis asks for necessary and sufficient conditions for integers k and m ≥ 2 such that a pair of latin squares of order n exists that intersect precisely in k disjoint m-flowers. The necessary terminology, constructions, lemmas and proof for this result are contained in Chapters 7, 8 and 9. The second such problem considered in this thesis asks for necessary and sufficient conditions for integers k such that a pair of Steiner triple systems of order u exists that intersect precisely in k disjoint 2-flowers. This result relies on the solution to the latin square problem and an additional result from Chapter 9. The further constructions and lemmas used to prove this result are detailed in Chapter 10.