Physics Commons^™

Modelling Cell Population Growth, Mahmood Mazarei

Electronic Thesis and Dissertation Repository

The growth of biological matter, e.g., tumor invasion, depends on various factors, mainly the tissue’s mechanical properties, implying elasticity, stiffness, or apparent viscosity. These properties are impacted by the characteristics of the tissue’s extracellular matrix and constituent cells, including, but not limited to, cell membrane stiffness, cell cytoskeleton mechanical properties, and the intensity and distribution of focal adhesions over the cell membrane. To compute and study the mechanical properties of tissues during growth and confluency, a theoretical and computational framework, called CellSim3D, was developed in our group based on a three-dimensional kinetic division model.

In this work, CellSim3D is …

Polymer Translocation Through A Nanopore: Controlling Capture Conformations Using An Electrical Force, Matthew D. Wei

Undergraduate Student Research Internships Conference

Solid-state nanopore sensors remain a promising solution to the rising global demand for genome sequencing. These single-molecule sensing technologies require single-file translocation for high resolution and accurate detection. This study uses molecular dynamics-lattice Boltzmann simulations of the capture of a single polymer chain under pressure-driven hydrodynamic flow to investigate a method of increasing the single-file capture and translocation rate. By using a model force of two oppositely electrically charged rings, single-file capture in hydrodynamic flow can be amplified from about 45% to 51.5%. This paper found that the optimal values of force location, force strength, and system pressure/flow velocity are …

The Journey Of A Single Polymer Chain To A Nanopore, Navid Afrasiabian

Electronic Thesis and Dissertation Repository

Single chain translocation has been eagerly studied for more than two decades due to its importance in biological processes and also, providing a better understanding of polymer dynamics. Polymer translocation can be divided into three stages of reaching the pore, entering the pore and passing through it. We study the delivery of the chain from the bulk to the entrance, which is called the capture process, for a single chain driven by hydrodynamic flow. Our molecular dynamics-lattice Boltzmann simulations show that the converging flow around the nanopore not only facilitates the process of finding the pore but also deforms the …

Studying Resting State And Stimulus Induced Bold Activity Using The Generalized Ising Model And Independent Component Graph Analysis, Sivayini Kandeepan

Electronic Thesis and Dissertation Repository

Although many technical advancements have been made, neuroscientists still struggle to explain the underlying behaviour of how brain regions communicate with each other to form large-scale functional networks. functional Magnetic Resonance Imaging (fMRI) has been commonly used to investigate changes between brain regions over time using the Blood Oxygen Level Dependent (BOLD) signal.

The goal of this thesis is to show the applicability of novel techniques and tools, such as the generalized Ising model (GIM) and the independent component graph analysis (GraphICA), to obtain information on the functional connectivity of populations with altered perception of consciousness. The GIM was used …

Effects Of Impurities On Calcium Oxalate Crystallization As Measured By Atomic Force Microscopy, Himasha Wijesekara

Electronic Thesis and Dissertation Repository

Calcium oxalate crystals are found in kidney stones as either calcium oxalate monohydrate (COM) or calcium oxalate dihydrate (COD). COM crystals are the most abundant form as they are thermodynamically more stable than COD crystals under physiological conditions. Certain aspartic acid-rich molecules such as osteopontin (OPN) are known to affect stone formation by inhibiting COM and COD growth. We have studied COM {010} and COD {100} faces in the presence of OPN, poly-aspartic acid (poly-ASP) and synthetic peptides derived from OPN to investigate the inhibitor mechanism.

We observed that poly-ASP preferentially inhibits one particular direction of {010} faces on COM …

Development Of A 1-Dimensional Data Assimilation To Determine Temperature And Relative Humidity Combining Raman Lidar Backscatter Measurements And A Reanalysis Model, Shayamila N. Mahagammulla Gamage

Electronic Thesis and Dissertation Repository

Water vapor is the most dominant greenhouse gas in Earth's atmosphere. It is highly variable and its variations strongly depend on changes in temperature. Atmospheric water vapor can be expressed as relative humidity (RH), the ratio of the partial pressure of water vapor in the mixture to the equilibrium vapor pressure of water over a flat surface of pure water at a given temperature. Liquid water can exist as super-cooled water for temperatures between 0C to -38C. Thus, RH can be measured either relative to water (RHw) or to ice (RHi). RHi measurements are important in the upper tropospheric region, …

Application Of The Optimal Estimation Method (Oem) To Retrieve Relative Humidity From Raman Lidar Backscatter Measurements., Shayamila N. Mahagammulla Gamage, Robert Sica, Alexander Haefele

Western Research Forum

Accurate measurements of relative humidity (RH) vertical profiles in the atmosphere is important for understanding the earth's weather and the climate system. RH represent the current state of the water vapor in the atmosphere with respect to the ambient air related to saturation. Even minor changes of the RH in the lower atmosphere has a large impact of the global circulation and cloud formation. Due to its high variability RH measurements in the lower atmosphere is significantly challenging. Raman lidar is one of the potential tools that can provide vertical profiles of RH. Typically, temperature and water vapor mixing ratios …

Calculating The Dimensionality Of The Brain, And Other Applications Of An Optimized Generalized Ising Model In Predicting Brain's Spontaneous Functions, Pubuditha M. Abeyasinghe

Electronic Thesis and Dissertation Repository

Understanding a system as complex as the human brain is a very demanding task. Directly working with structural and functional neuroimaging data has led to most of the understanding we have gained about the human brain. However, performing only the direct statistical comparisons on the empirical function and the structure does not fully explain the observed long-range functional correlations. Therefore, implementations of mathematical models to gain further understanding of the relationship between the structure and function of the brain is critical. Additionally, spontaneous functions of the brain can only be predicted using computer simulated models; which will be pivotal for …

Vibrating-Wire Rheometry, Cameron C. Hopkins

Electronic Thesis and Dissertation Repository

This thesis consists of two projects on the behaviour of a novel vibrating-wire rheometer and a third project studying the gelation dynamics of aqueous solutions of Pluronic F127. In the first study, we use COMSOL to perform two-dimensional simulations of the oscillations of a wire in Newtonian and shear-thinning fluids. Our results show that the resonant behaviour of the wire agrees well with the theory of a wire vibrating in Newtonian fluids. In shear-thinning fluids, we find resonant behaviour similar to that in Newtonian fluids. In addition, we find that the shear-rate and viscosity in the fluid vary significantly in …

Dynamics Of Discs In A Nematic Liquid Crystal, Alena Antipova

Electronic Thesis and Dissertation Repository

In this thesis, a new way of simulating a two-way coupling between a liquid crystal and an immersed object is proposed. It can be used for objects of various geometries and can be expanded to be used for an object of any geometry. Additionally, a simple yet effective model was suggested for calculations of transmitted light through a nematic liquid crystal sample. This model allowed us to clarify the behavior of a ferromagnetic disc in a nematic liquid crystal observed in experiments and incorrectly interpreted at that time.

Our simulations have demonstrated the following: in the absence of external forces …

Simulation Of Heterogeneous Colloidal Particles Immersed In Liquid Crystals, Setarehalsadat Changizrezaei

Electronic Thesis and Dissertation Repository

This thesis describes an investigation of interactions between colloidal particles immersed in a liquid crystal. The presence of colloidal particles in the liquid crystal distorts the director field distorted from its uniform orientation. These elastic distortions produce topological defects around the particles, which induce anisotropic interactions between them, and these anisotropic interactions can be used to manufacture non-closed packed colloidal crystals, such as diamond lattices, which are interesting in photonic applications. First, different types of liquid crystals, the mathematical tools to describe the anisotropic nature of liquid crystals, the Landau-de Gennes free-energy model to investigate the particle’s interaction, and different …