Theses, Dissertations and Student Research Papers (Physics)http://hdl.handle.net/1957/180702016-02-07T10:47:16Z2016-02-07T10:47:16ZMonte Carlo simulations for a soft sphere fluidKreitzberg, Patrickhttp://hdl.handle.net/1957/560782015-06-10T14:15:06Z2015-05-08T00:00:00ZMonte Carlo simulations for a soft sphere fluid
Kreitzberg, Patrick
In this paper I present the results of Monte Carlo simulations for a soft sphere fluid with a Weeks-Chandler-Anderson (WCA) pair potential. The results are compared to Soft Fundamental Measure Theory (SFMT) results obtained by our research group. One of the research group’s goals was to show that our SFMT is accurate over a wide range of reduced temperatures and densities. The radial distribution function and pressure calculations were accurate at temperatures below freezing and higher than room temperature as well as reduced densities ranging from 0.3 to 1.0. Experimental data for the radial distribution function of argon was matched very well using a soft-sphere fluid surrounding a sphere with a Leonard-Jones pair potential.
2015-05-08T00:00:00ZNucleation of Iron Dust From Type II SupernovaeFletcher, Lisahttp://hdl.handle.net/1957/560422015-06-09T14:08:17Z2015-06-08T00:00:00ZNucleation of Iron Dust From Type II Supernovae
Fletcher, Lisa
When a star dies in a supernova, its constituent particles are torn apart and a gaseous cloud of atoms remains. These atoms may eventually condense again into large bodies such as planets and stars. There are three main theories as to how this happens: classical, kinetic, and non-local thermodynamic equilibrium (non-LTE). In the classical theory, no nucleation can occur below a critical density and saturation and does not account for much of the nucleation that must occur in the interstellar medium(ISM). The kinetic and non-LTE theories allow for nucleation to occur below the classical critical levels. Most research into this area so far has been focused on the formation of carbon dust. Carbon has a very specific geometry and behaves rather uniquely from a chemical perspective. I was curious as to how a difference in atomic geometry and chemical behavior would affect the formation of dust particles. To investigate this, I am studying the formation of iron dust in supernova remnants. The assumptions that the iron in the supernova remnants exists solely as individual atoms, that the iron atoms are spherical, and that cloud is composed solely of iron atoms all simplified the initial results. Once reasonable results are obtained with these assumptions, they may be removed in order to get a more realistic picture of the formation of iron dust.
2015-06-08T00:00:00ZComparison of a Persistent Random Walk to 3D Chemo taxis in MDA-MB-231 Cancer CellsThayer-Freeman, Cameronhttp://hdl.handle.net/1957/560352015-06-09T13:24:46Z2015-06-08T00:00:00ZComparison of a Persistent Random Walk to 3D Chemo taxis in MDA-MB-231 Cancer Cells
Thayer-Freeman, Cameron
This research specifically examines the collective motion of populations of MDA-MB-231 breast cancer cells under the influence of a chemo-attractant gradient. Their motion is compared to the mathematical model of a persistent random walk, measuring the persistence bias of the cells from their autocorrelation function and applying to the mean squared distribution function predicted by the persistent random walk model. The motion of cells within the population is also analyzed; comparing free and caged cancer cell motion to the model of a persistent random walk. The results show strong evidence towards the conclusion that the collective motion of breast cancer cells does not fit into the model of a persistent random walk.
2015
2015-06-08T00:00:00ZFramework for Computational Modelling of Cellular Diffusion SystemsSenger, Mitchell Johnhttp://hdl.handle.net/1957/560342015-06-09T13:15:29Z2015-05-08T00:00:00ZFramework for Computational Modelling of Cellular Diffusion Systems
Senger, Mitchell John
Many biological processes are regulated by the presence and movement of cellular Ca²⁺ ions. The concentration of Ca²⁺ in a cellular environment is regulated by IP₃ sensitive channels that lie on the surface of a cell’s endoplasmic reticulum. Little is known about the macroscopic effects of intracellular Ca²⁺ activity, so these processes are of key interest to the field of experimental biophysics. Experiments that study macroscopic processes that result from intracellular Ca²⁺ action are difficult to conduct in a lab, so a computational simulation that accurately simulates ion diffusion within a multicellular system is a key tool for studying the large scale effects of intracellular Ca²⁺ fluctuations.
The product of this thesis is a computational framework for intracellular ion diffusion that will be used as the basis for modeling of multicellular systems in the future. This model generates a spatial boundary from a cell image and overlays a grid comprised of rectangular boxes suitable for discretized diffusion calculations on the cell space. Simulations of particle movement are performed by calculating the particle flux through the boundaries of each box in the grid using Fick’s laws of diffusion. An adaptive gridding method has been developed to increase the accuracy of the representation of cellular structures within the grid while greatly increasing calculation efficiency. Efficiency differences between simulations using the adaptive and non-adaptive gridding techniques have been analyzed.
2015
2015-05-08T00:00:00Z