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DNA scaffolds self-assembled by short-stranded synthetic DNA can be tailored to build thermally reversible hydrogels with target binding sites. These hydrogels exhibit highly selective binding properties due to the specificity of DNA and also provide an aqueous environment for various reactions to happen within the network constraints. Hence, a careful study on the assembly mechanism and other physical aspects of DNA hydrogels is required to facilitate the future design and construction of such materials at the precise control. In this thesis, I present the work on well-designed DNA nano-stars as scaffolds for functional bulk materials with potential applications in bio-sensing. Chapter 1 starts with introducing the fundamental properties of DNA molecules, focusing on the advantages of utilising short-stranded DNA to programme and engineer micro- and macro- materials. Then it briefly reviews the field of rheology and micro-rheology, with the diffusing wave spectroscopy (DWS) technique illustrated explicitly as an example passive micro-rheology tool. Afterwards, a critical literature review on computational modelling of DNA systems is present, followed by the thesis outline at the end. Chapter 2 describes a simple DNA dendrimer system self-assembled from three-armed DNA nano-stars. The characterisation tools such as UV-vis spectroscopy, gel electrophoresis and dynamic light scattering (DLS) are introduced to verify the final production of the complex DNA structures. From this practice, we develop a routine for designing DNA scaffolds that yield optimal productivity. Chapter 3 investigates the mechanical properties of DNA hydrogels made of three-armed DNA nano-stars and how they change upon cooling and heating empolying DWS micro-rheology. The resulting viscoelastic moduli over a broad range of frequencies reveal a clear, temperature-reversible percolation transition coinciding with the melting temperature of the system's sticky ends. This indicates that we can achieve precise control in mechanical properties of DNA hydrogels, which is beneficial for designing more sensitive molecular sensing tools and controlled release systems. Chapter 4 develops a coarse-graining computational model of DNA hydrogels that resembles the system in Chapter 3 using LAMMPS, a classical molecular dynamics code. Thermodynamics, structural analysis and rheology tests were taken, qualitatively reproducing the physical phenomena of DNA assembly of the hydrogel network. Chapter 5 studies the internal behaviours of three-armed DNA complexes using oxDNA model also implemented in LAMMPS, with particular focus on the effect of the inert bases in the core and between double-stranded branches and single-stranded sticky ends. A deep insight into sequence-dependent behaviour of such complex structures can guide the parameter optimisation of the individual building blocks for the model described in Chapter 4. Chapter 6 concludes the thesis and presents an outlook for the future work that emerged out of my experimental and numerical studies.

Bioactive glass is a type of third generation bioactive material that can bond to both soft and hard tissue with applications ranging from bone defect repair, coatings for metallic implants, to scaffolds for tissue engineering. Design of bioactive glasses for these applications rely on a detailed understanding of the structures of these glasses which are complicated and multicomponent. In this thesis, I have applied molecular dynamics (MD) simulations with interatomic potentials developed in our group to understand the effect of modifier cation substitution on the structures and properties of two series of bioactive glasses. Particularly, MD simulations are used to understand K2O to Na2O and MgO to CaO substitution on the short and medium range structures (such as cation coordination number, pair distribution function, Qn distribution, and ring size distribution) and properties (such as bulk and Young's moduli and CTE) of 55S4.1 bioactive glasses. As Na2O is incrementally substituted with K2O in 55S4.1, a decrease of the glass transition temperature (Tg) and an increase of CTE was observed, as well as a decreasing trend in the moduli. For the MgO to CaO substitution series, Mg2+ is mainly four-fold coordinated that suggests that it can play a role as a network former in this series. Results of both series showed characteristics of the phenomena of the mixed alkali effect (MAE) that has been known to show non-linear variations in trends like Tg in glasses with alkali and alkali earth ion substitution.

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The aim of this thesis work is to increase the knowledge of phenomena taking place during the initial stage in a top blown converter. The work has been done in a few steps resulting in four different supplements. Water model experiments have been carried out using particle image velocimetry (PIV) technology. The system investigated was a fundamental top blown converter where an air jet was set to impinge on a water surface. The flow field of the combined blown case, where an air jet was introduced through a bottom nozzle, was also captured by the PIV. The work clearly showed that the flow field caused by an impinging top blown jet alone could not match that of the bottom blown case. The main re-circulation loop (or vortex) was investigated with respect to position and it was found that an increased flow rate pushes the center of the re-circulation loop downwards into the bath. However, for the top-blown case there is a point when the flow rate is too large to cause a distinguishable re-circulation loop since the jet becomes more plunging (i.e. penetrates deep into the bath) than impinging, with large surface agitation and splashing as a result.A numerical model with the same dimensions as the experimental system was then created. Three different turbulence models from the same family were tested: standard-, realizable- and a modified-(slight modification of one of the coefficients in order to produce less spreading of the air jet) k-ε turbulence model. It could be shown that for the family of k-ε turbulence models the difference in penetration depth was small and that the values corresponded well to literature data. However, when it comes to the position of the re-circulation loop it was shown that the realizable k-ε model produced better results when comparing the results to the experimental data produced from the PIV measurements, mentioned earlier.It was then shown how the computational fluid dynamics (CFD) model could be coupled to thermodynamics databases in order to solve for both reactions and transport in the system. Instead of an air-water system, a gas-steel-slag system was created using the knowledge obtained in the previous simulation step described above. Reactions between gas-steel, gas-slag, steel-slag and gas-steel-slag were considered. Extrapolation of data from a few seconds of simulation was used for comparison to experimental data from the literature and showed reasonable agreement. The overall conclusion was that it is possible to make a coupling of the Thermo-Calc databases and a CFD software to make dynamic simulations of metallurgical processes such as a top-blown converter.A parametric study was then undertaken where two different steel grades were tested; one with high initial carbon content (3.85 mass-%) and one with lower carbon content (0.5 mass-%). The initial silicon content was held constant at 0.84 mass-%. Different initial temperatures were tested and also some variation in initial dissolved oxygen content was tried. It was found that the rate of decarburization/desiliconization was influenced by the temperature and carbon concentration in the melt, where a high temperature as well as a high carbon concentration favors decarburization over desiliconization. It was also seen that the region affected by a lower concentration of alloys (or impurities) was quite small close to the axis where the impinging jet hits the bath. Add the oscillating nature of the cavity and it was realized that sampling from this region during an experiment might be quite difficult. / QC 20100720

This thesis presents results of computations of supersonic flow over finite cylinders with varying geometries at the cylinder-wall juncture. The flow domain and geometries were modeled after experiments conducted at University of Tennessee Space Institute (UTSI). CREATE Kestrel (KCFD) was used to perform improved-delayed detached simulations (IDDES) of the unsteady flow. Time-accurate data were collected via taps along the centerline partially on the surface of the cylinder geometries and on the wall upstream of the cylinder. Spectra of the pressure signals and two-point correlations were computed to compare the flow between the different cases consisting of a baseline cylinder, the cylinder with a smaller gap, and the cylinder with a wider fairing. Properties on the cylinder surface for the gap case had the greatest difference compared to the others. In addition, the spectral content showed higher frequency activity for the gap case on the surface in front of the cylinder. <br>

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Solar PV-based distributed generation has increased significantly over the last few years, and the rapid growth is expected to continue in the foreseeable future. As the penetration levels of distributed generation increase, power systems will become increasingly decentralized with bi-directional flow of electricity between the transmission and distribution networks. To manage such decentralized power systems, planners and operators need models that accurately reflect the structure of, and interactions between the transmission and distribution networks. Moreover, algorithms that can simulate the steady state and dynamics of power systems using these models are also needed. In this context, integrated transmission and distribution system modeling and simulation has become an important research area in recent years, and the primary focus so far has been on studying the steady state response of power systems using integrated transmission and distribution system models. The primary objective of this dissertation is to develop an analysis approach and a program that can simulate the dynamics of three phase, integrated transmission and distribution system models, and use the program to demonstrate the advantages of evaluating the impact of solar PV-based distributed generation on power systems dynamics using such models. To realize this objective, a new dynamic simulation analysis approach is presented, the implementation of the approach in a program is discussed, and verification studies are presented to demonstrate the accuracy of the program. A new dynamic model for small solar PV-based distributed generation is also investigated. This model can interface with unbalanced networks and change its real power output according to the incident solar irradiation. Finally, application of the dynamic simulation program for evaluating the impact of solar PV units using an integrated transmission and distribution system model is discussed. The dissertation presents a new approach for studying the impact of solar PV-based distributed generation on power systems dynamics, and demonstrates that the solar PV impact studies performed using the program and integrated transmission and distribution system models provide insights about the dynamic response of power systems that cannot be obtained using traditional dynamic simulation approaches that rely on transmission only models. / Ph. D.

In this study, dynamic crack propagation in brittle materials has been studied using a regularized phase field approach.The phase field model used has been validated using specific experimental results of a dynamic in-plane fracture. The crack branching phenomena and existence of a limiting crack tip velocity has been validated using a mode I simulation set-up. A parametric study has also been performed so as to normalize the various numerical parameters that affect the velocity at the crack tip. Following the validation of the phase field model a stochastic analysis of a PBX microstructure has been performed. The microstructure has a high HMX volume fraction of 79\%. The energetic material is HMX and the binder used is Sylgard. Artificial defects are introduced in the system using phase field cracks. The analysis uses a finite element framework that accounts for various thermal-mechanical processes like deformation, heat generation, conduction, fracture and frictional heating at the crack surfaces. The effect on the temperature and damage field due to varying parameters like loading velocities and critical energy release rates is studied. Critical hotspot formation due to localized frictional heating is also studied. A concept of dirty binder is introduced to increase the grain volume fraction of the energetic in the composite. This amounts to a homogenized binder that accounts for the influence of the subsume particles that do not contribute to fracture but affect material properties of the binder.

Apresentamos uma série de estudos, baseados em simulações de Dinâmica Molecular no vácuo e em solução, sobre o processo de complexação das supramoléculas tetraethylester p-tert-butyl calix[4]arene (CLE) e tetramethylketone p-tert-butyl calix[4]arene (CLC) com os íons Pb2+ e Cd2+ e espécies neutras. Os modelos para as moléculas de calixareno e do solvente foram baseados no campo de forças OPLS-AA. Os parâmetros para os íons foram desenvolvidos a partir de uma metodologia de ajuste de valores de modo a reproduzirem simultaneamente propriedades termodinâmicas e estruturais obtidas experimentalmente ou por cálculos de QM/MM. As simulações no estado líquido nos mostraram que o CLE aprisiona os íons de maneira mais eficiente que o CLC, formando complexos mais estáveis. A complexação do íon desencadeia um efeito alostérico em ambos os calixarenos estudados, permitindo a complexação de uma molécula de acetonitrila na cavidade hidrofóbica estabilizando o complexo. Nas simulações com o CLC observamos que a complexação da acetonitrila é necessária para manter o íon ligado à cavidade hidrofílica, evidenciando a dependência desses complexos com esse solvente em específico. Apesar de observarmos que o CLE apresenta maior afinidade com os íons Pb2+ e Cd2+ que o CLC, somente futuras simulações utilizando a água como solvente poderão confirmar a viabilidade do uso desta molécula em sistemas destinados à despoluição ambiental. / We report a series of Molecular Dynamics simulations, in vacuum and in acetonitrile solution, on the complexation process of the calixarens tetraethylester p-tert-butyl calix[4]arene (CLE) and tetramethylketone p-tert-butyl calix[4]arene (CLC) with Pb2+ and Cd2+ anions and neutral species. The solvent and calixarene molecules were modeled based on the OPLS-AA force field. The parameters for the ions were adjusted to simultaneously reproduce some structural and thermodynamic properties obtained either experimentally or from QM/MM calculations. The simulations in the liquid phase show CLE to be more efficient than CLC in trapping the studied metal ions, leading to more stable complexes. Ion complexation gives rise to an allosteric effect by which a solvent molecule is trapped in the hydrophobic cavity giving rise to further stabilization of the complex. Simulations on CLC show that formation of the calixarene-acetonitrile adduct is essential to the stabilization of the ionic complex, thus exhibiting the influence of this particular solvent in the very existence of the complex. In spite of the conclusion that CLE has higher affinity than CLC for Pb2+ and Cd2+ ions, only further studies in water solution will permit to evaluate the real potential of this molecule as an efficient scavenger of environmental heavy metal pollution.