Fluoropolymers are employed in countless end-user applications across several industries. One such fluoropolymer is polytetrafluoroethylene. This research is concerned with studying and understanding the thermal behavior of polytetrafluoroethylene. Such understanding is critical to predict its behavior in diverse service environments as the polymer ages and for allowing bottom up design of improved polymers for specific applications. While a plethora of experiments have investigated the thermal properties of polytetrafluoroethylene, examining these properties using molecular dynamics simulations remains in its infancy. In particular, the current body of molecular dynamics research on polytetrafluoroethylene has primarily focused on studying polytetrafluoroethylene phases, its physical nature, and its helical conformational structure. The present study is the first molecular dynamics simulations research to study polytetrafluoroethylene behavior near the glassy transition temperature. Specifically, the current research utilizes molecular dynamics simulations to achieve the following objectives: (a) model and predict polytetrafluoroethylene glassy transition temperature at different molecular weights, (b) examine the impact of glassy transition temperature on the volume-temperature and thermal properties, (c) study the influence of molecular weight on polytetrafluoroethylene melt and glassy state, and (d) determine the governing forces at the molecular level that control polytetrafluoroethylene glassy transition temperature. Achieving the aforementioned objectives requires performing four major tasks. Motivated by the scarcity of polytetrafluoroethylene force fields research, the first task aims to generate and test polytetrafluoroethylene force fields. The parameters were produced based on the Optimized Potentials for Liquid Simulations All Atom model. The intramolecular parameters were generated using the automated frequency matching method while the torsional terms were fitted using the nonlinear least squares algorithm. The intermolecular partial atomic charges were obtained using Northwest Computational Chemistry software and fitted using the restrained electrostatic potential at (MP2/6-31G*) level of theory. The final set of parameter was tested by calculating polytetrafluoroethylene density using molecular dynamics simulations. The second task involves building polytetrafluoroethylene amorphous structure using molecular dynamics at periodic boundary conditions for polytetrafluoroethylene cell at different molecular weights. We use the amorphous structure in the molecular dynamics simulations in consistence with research evidence which reveals that polymer properties such as the specific volume will differ as the polymer passes the glassy transition when it is in the amorphous phase structure whereas no variation occurs when the polymer passes the glassy transition while it is in the crystalline structure. The third task includes testing polytetrafluoroethylene melt phase properties: density, specific heat, boiling point, and enthalpy of vaporization. In the fourth and final task, we performed molecular dynamics simulations using NAnoscale Molecular Dynamics program. This task involves the polymer relaxation process to predict polytetrafluoroethylene mechanical behavior around the glassy transition temperature. Properties that are affected by this transition such as density, heat capacity, volumetric thermal expansion, the specific volume, and the bulk modulus were examined and the simulated results were in good agreement with experimental findings.

The High Level Architecture (HLA) provides a universal solution for interconnecting various simulation environments and applications thus creating a more complex simulation entity. The idea is built upon controlled and directed data exchanges of objects and events (via the RunTime Interface - RTI) shared by participants (i.e. simulations) thus creating a distributed data environment. The aim of this thesis is to investigate usability of HLA for agent based development platforms (e.g. Pogamut) as well as providing transparent and simple to use access to HLA for HLA unaware applications. The thesis describes architecture and provides a prototype proof-of-concept implementation, which integrates HLA with two different (closed source) game engines providing them the ability to communicate to a simple client application according to a reasonable subset of the HLA standard. The thesis also provides performance measurements of prototype implementation.

The number of three-dimensional structures of potential protein targets available in several platforms such as the Protein Data Bank is subjected to a constant increase over the last decades. This observation should be an additional motivation to use structure-based methodologies in drug discovery. In the recent years, different success stories of Structure Based Drug Design approach have been reported. However, it has also been shown that a lack of druggability is one of the major causes of failure in the development of a new compound. The concept of druggability can be used to describe proteins with the capability to bind drug-like compounds. A general consensus suggests that around 10% of the human genome codes for molecular targets that can be considered as druggable. Over the years, the protein druggability was studied with a particular interest to capture structural descriptors in order to develop computational methodologies for druggability assessment. Different computational methods have been published to detect and evaluate potential binding sites at protein surfaces. The majority of methods currently available are designed to assess druggability of a static structure. However it is well known that sometimes a few local rearrangements around the binding site can profoundly influence the affinity of a small molecule to its target. The use of techniques such as molecular dynamics (MD) or Metadynamics could be an interesting way to simulate those variations. The goal of this thesis was to design a new computational approach, called JEDI, for druggability assessment using a combination of empirical descriptors that can be collected ‘on-the-fly’ during MD simulations. JEDI is a grid-based approach able to perform the druggability assessment of a binding site in only a few seconds making it one of the fastest methodologies in the field. Agreement between computed and experimental druggability estimates is comparable to literature alternatives. In addition, the estimator is less sensitive than existing methodologies to small structural rearrangements and gives consistent druggability predictions for similar structures of the same protein. Since the JEDI function is continuous and differentiable, the druggability potential can be used as collective variable to rapidly detect cryptic druggable binding sites in proteins with a variety of MD free energy methods.

Previous investigations of FePd circular island arrays have shown the hysteresis-free switching from vortex to collinear magnetic state at high temperatures [1]. This raises interest in the exploration of the temperature and inter-island interaction effect on the magnetization dynamics in this kind of structures. Ferromagnetic resonance (FMR) measurements allow for the investigation of the magnetization response to time-dependent magnetic field excitations. In this work, the dynamics of a square lattice of circular Fe20Pd80 alloy islands were investigated. The micromagnetic simulations of FMR response were carried out with the parameters similar to those used in the experiments. The experimentally measured FMR absorption spectra were qualitatively reproduced employing micromagnetic simulations. Furthermore, the spatial maps of th estanding spin wave modes were calculated. It was confirmed that the features arising in the FMR absorption spectra are governed by both the temperature and the inter-island interactions.

In the UCNτ experiment, ultracold neutrons (UCN) are confined by magnetic fields and the Earth’s gravitational field. Field-trapping mitigates the problem of UCN loss on material surfaces, which caused the largest correction in prior neutron experiments using material bottles. However, the neutron dynamics in field traps differ qualitatively from those in material bottles. In the latter case, neutrons bounce off material surfaces with significant diffusivity and the population quickly reaches a static spatial distribution with a density gradient induced by the gravitational potential. In contrast, the field-confined UCN—whose dynamics can be described by Hamiltonian mechanics—do not exhibit the stochastic behaviors typical of an ideal gas model as observed in material bottles. In this report, we will describe our efforts to simulate UCN trapping in the UCNτ magneto-gravitational trap. We compare the simulation output to the experimental results to determine the parameters of the neutron detector and the input neutron distribution. The tuned model is then used to understand the phase space evolution of neutrons observed in the UCNτ experiment. We will discuss the implications of chaotic dynamics on controlling the systematic effects, such as spectral cleaning and microphonic heating, for a successful UCN lifetime experiment to reach a 0.01% level of precision.

Thesis advisor: Krzysztof Kempa / In my work presented in this dissertation, I have focused on simulation studies of light interaction with nanostructures made of metals and dielectrics. Of particular interest have been plasmonic effects. The structures included the wire and coaxial nanowaveguides, as well as periodic arrays of planar quasi-triangles, and periodic arrays of nanoholes in thin metallic films. In the nanowaveguides I focused on plasmon polariton modes which resemble the TEM modes propagating in the corresponding conventional radio transmission lines. This collaborative research, involving an experimental effort, showed how the nanoscopic plasmon polariton modes reduce in the retarded limit to the TEM modes, and in the non-retarded limit to the corresponding surface plasmon modes. My simulations explained details of recent experimental results involving plasmonic waveguiding in metallic nanowires. Similar results have been obtained for nanocoaxial waveguides. My simulations of the optical absorption in the arrays of nano quasi-triangles, recently observed experimentally, helped identify those as due to Mie plasmonic resonances in these nanoparticles. They also explained the peak shifts in terms of the 2D surface plasmon dispersion, and the plasmon momentum quantization. In the study of the arrays evolution from holes to quasi-triangles, my simulations provided the clue to the critical behavior of the peak position for structures approaching the percolation threshold (the transitional structure in the series, for which film resistance diverges), and allowed to identify the series of structures as an analog of the percolation threshold problem. Finally, I have simulated optical performance of nanorod arrays (or multi-core nanocoax), which have been employed as platform for novel solar cells. My simulations have been employed to predict and optimize these cells. My work resulted in 5 publications and 2 manuscripts in preparation. / Thesis (PhD) — Boston College, 2011. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Physics.

No presente trabalho estudamos a difusão de compostos dispersos atmosfericamente como, por exemplo, fertilizantes e pesticidas particulares, em ambientes agrícolas de larga escala. Tal estudo foca-se na aplicabilidade de modelos numéricos e teórico-fenomenológicos de fenômenos turbulentos em estimativas de vantagens econômica e ambiental desses sistemas. A atmosfera terrestre, em escalas de tamanho e velocidade típicas do objeto de estudo deste trabalho, é um sistema turbulento. A turbulência é um fenômeno complexo, que envolve a interação dinâmica de distintas escalas resultando em um efeito coletivo de larga escala, decorrente de uma interação não linear entre modos perturbativos em um fluido. A modelagem da turbulência, portanto, é em geral possível através de Simulação Numérica Direta - DNS (Direct Numeric Simulation). Uma das consequências típicas da turbulência é a difusão, ou seja, o aumento em sistemas abertos da separação entre corpos particulados, em taxas muito superiores àquelas da difusão molecular térmica padrão. Neste trabalho, apresentamos um estudo focado na quantificação da difusão turbulenta de partículas através de simulações numéricas de turbulência, com o objetivo de identificar impactos de fertilização e dispersão de poluentes atmosféricos com implicações na saúde e ambiente / In the present study, we study the diffusion dispersed atmospherically compounds, such as fertilizers and particular pesticides in large scale agricultural environments. This study focuses on the applicability of numerical and theoretical and phenomenological models of turbulent phenomena in estimates of economic and environmental advantages of these systems. The Earth\'s atmosphere, in typical size and speed ranges of the study object of this work is a turbulent system. Turbulence is a complex phenomenon which involves the dynamic interaction of different ranges resulting in a large-scale collective effect due to a nonlinear interaction between perturbation modes in a fluid. The modeling of turbulence, so it is generally possible through Direct Numerical Simulation - DNS. A typical consequence of turbulence is the diffusion, i.e., increased separation in unbound systems of particulate bodies, much higher than those of the standard thermal molecular diffusion rates. In this work we present a study focused on quantifying the turbulent diffusion of particles through numerical simulations of turbulent media, in order to identify the impact of fertilization and dispersion of air pollutants on human health and environment

Uma parcela considerável do consumo energético, e consequentemente, dos custos das operações de tratamento de minérios é atribuída a cominuição. O High Pressure Grinding Rolls (HPGR) surge com o apelo de eficiência energética, o que, potencialmente, reduziria os custos operacionais. Nesta pesquisa, esta tecnologia é analisada como uma alternativa à rota convencional de cominuição de óxido de alumínio eletrofundido de um empreendimento em particular, que compreende um complexo circuito de britadores de rolos. Duas amostras de óxido de alumínio eletrofundido, denominadas BT e TB, foram submetidas a ensaios de HPGR (circuito aberto) e de caracterização física (DWT, WI, AI, densidade). Adicionalmente, foram realizadas simulações no software JKSimMet® 6.0 com o objetivo de prever o desempenho do equipamento em circuito fechado e realizar o escalonamento da unidade industrial. As distribuições granulométricas dos produtos dos ensaios de HPGR em circuito aberto e as distribuições granulométricas dos produtos dos circuitos fechados de HPGR simulados foram comparadas às granulometrias do produto requeridas pelo circuito industrial. Avaliou-se, também, o atendimento da vazão mássica requerida. Os resultados demonstram que a rota alternativa baseada no HPGR oferece um expressivo potencial de simplificação do circuito, com uma redução considerável do número de equipamentos de cominuição de 13 para 1, o que, além de, possivelmente, impactar na redução de custos operacionais, facilita o controle da operação. / A considerable portion of energy consumption and, as a consequence, operational costs in mineral processing is associated with comminution. High Pressure Grinding Rolls (HPGR) are appealing for their energy efficiency, which would potentially reduce operating costs. This study evaluates this technology as an alternative to the conventional electrofused aluminum oxide comminution route of a specific plant comprising a complex roll crushing circuit. Two electrofused aluminum oxide samples, called BT and TB, were submitted to HPGR (open circuit) and physical characterization (DWT, WI, bulk density, specific gravity) tests. In addition, simulations were conducted using JKSimMet® 6.0 software, aiming to predict the performance of a closed-circuit equipment and scale-up of an industrial scale unit. Product size distributions of the open-circuit HPGR tests and closed circuit HPGR simulations were compared with the product size distribution required by industrial comminution circuit. The required throughput was also evaluated. Results show that the alternative HPGR route provides a remarkable potential for circuit simplification, while considerably reducing the number of comminution equipments from 13 to 1, which facilitates operational control and possibly reduces operating costs.

Advances in molecular-simulation methods allow for ever larger systems of particles to be studied and on longer timescales. Calculations are reaching such a scale that they can be used to address a vast range of key questions across chemistry, physics, and engineering. In this work, molecular dynamics and Monte Carlo simulations are employed to address two key areas: the structure and dynamics of simple aqueous ionic salt solutions at high concentrations; and the structure, dynamics, and phase behaviour of dipolar fluids (such as colloidal ferrofluids). The first part of the work begins with a study of the structure and dynamics in metastable, supersaturated, aqueous solutions of potassium chloride, and the possible relevance of these to the phenomenon of non-photochemical laser-induced nucleation (NPLIN). It is thought that the potassium and chloride ions form long-lived, amorphous clusters that may, under the influence of nanosecond laser pulses, undergo structural reorganisation to form post-critical crystal nuclei. It is found that spontaneous nucleation does not occur on the simulation timescale, but that amorphous clusters do form with cluster lifetimes comparable to those of the shortest laser pulses that can be used in NPLIN ( 100 picoseconds). Next, an alternative scenario for NPLIN involving rapid laser heating of impurity particles is examined by simulating heated carbon nanoparticles in saturated aqueous solutions of sodium chloride. The concentration at which an aqueous sodium chloride solution first crystallises on the simulation timescale is determined. A spherical carbon impurity is then added to a system with concentration close to, but lower than, the concentration at which crystallisation occurs on the simulation timescale. The effects that adding, and heating, this impurity has on the structure of this near-crystallising system are then observed. The second part of the work discusses model dipolar fluids, of direct relevance to colloidal ferrofluids (suspensions of magnetised nanoparticles in simple carrier liquids). The two-body, dipole-dipole interaction is long-ranged and anisotropic, and it is computationally expensive to handle in molecular simulations. Here a new method is proposed that relies on a formal mapping between the partition function of a dipolar fluid and that of a hypothetical fluid with many-body, short-ranged, isotropic interactions. Only the leading-order two-body interactions (akin to the van der Waals attraction) and three-body interactions (corresponding to the Axilrod-Teller potential) are retained. It is shown that this simple model is sufficient to reproduce the characteristic particle chaining and the associated disappearance of the vapour-liquid phase transition of dipolar fluids. Finally, the dynamical response of ferrofluids to oscillating magnetic fields (the dynamic magnetic susceptibility [DMS]) is studied. The DMS of ferrofluids, predicted by a new theory that takes into account the leading-order effects of dipole-dipole interactions, are critically compared to those found using Brownian-dynamics simulations of monodisperse systems of dipolar particles. This new theory is found to provide more accurate predictions of the DMS than previous theories, with the DMS predicted to a high degree of accuracy for systems with dipolar coupling strength in the experimentally achievable region.

In this thesis I investigate the role of spatial structure, cell-cell interactions and horizontal gene transfer on the genetic composition of growing microbial colonies. In the first part I study how the roughness of the growing layer of the colony depends on the shape of colony-forming cells. To study its impact I develop an off-lattice Eden-like model in which cells are represented as spherocylinders with a variable aspect ratio. I show that the roughness of the expansion front is not significantly affected by the shape of cells and that the dynamic scaling of growing front belongs to the KPZ universality class. Roughness is an important and easy to measure feature which affects the probability of fixation of genetic lineages in the colony. Another feature contributing to the genetic composition of a microbial community is horizontal gene transfer, which is investigated in the second part of this thesis. I develop an agent-based computational model of bacterial cells which grow, divide, and interact mechanically. I focus on plasmid conjugation, in which donors transfer a plasmid (a small, circular DNA molecule) to plasmid-free recipients. I show that bacteria in the expanding colony segregate into sectors of donors and acceptors. Donor sectors grow at the expense of acceptor sectors and that effect can be effectively described by coalescing random walkers that perform biased random walk on the colony expansion front. I use numerical and analytical methods to show that the plasmid eventually spreads to the whole colony given enough time, and I also show that this time is unrealistically long for experimentally determined conjugation rates and therefore real colonies are expected to have both acceptor and donor sectors. Furthermore, my simulations show that segregative plasmid loss at the moment of cell division can counteract the effect of conjugation and can lead to fixation of plasmid free cells. I also show that changes in nutrient concentration and the resultant change in roughness of the expansion front affect the rate of plasmid spread into population. Quantitative and qualitative results obtained in this section may serve as a tool to extract plasmid invasion rates from experimental data. In the last part of this thesis I investigate how the physical factors, such as finite strength of conjugative junctions, affect the conjugation process. I develop a computational model of plasmid transfer in which conjugative junctions are explicitly modelled as short, spring-like tubes that connect conjugating cells. My results show that factors such as junction creation rate and its strength can significantly affect the conjugation performance. I study different situations corresponding to different experimental scenarios (well-mixed colony on a filter paper, colliding colonies) and show that shear forces acting between cells can significantly lower the rate of plasmid transfer. My results can explain why conjugation occurs very rarely in some of these scenarios investigates in laboratory assays.