Biological and Chemical 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 …

A Molecular Dynamics Study Of Polymer Chains In Shear Flows And Nanocomposites, Venkat Bala

Electronic Thesis and Dissertation Repository

In this work we study single chain polymers in shear flows and nanocomposite polymer melts extensively through the use of large scale molecular dynamics simulations through LAMMPS. In the single polymer chain shear flow study, we use the Lattice Boltzmann method to simulate fluid dynamics and also include thermal noise as per the \emph{fluctuation-dissipation} theorem in the system. When simulating the nanocomposite polymer melts, we simply use a Langevin thermostat to mimic a heat bath. In the single polymer in shear flow study we investigated the margination of a single chain towards solid surfaces and how strongly the shear flow …

Comparing Semi-Automated Segmentation Of Traditional-Resolution And High-Resolution Hyperpolarized 129xe Mri On Covid-19 Survivors, Tingting Wu

Undergraduate Student Research Internships Conference

Hyperpolarized gas MRI using inert gases like Xe is a valuable tool in visualizing lung ventilation in patients, and can be used as a longitudinal monitoring tool for patients with lung diseases. However, use of this method requires segmentation and quantification of parameters such as ventilation defect percentage (VDP), which is often very subjective depending on the observer. This study aimed to determine the accuracy and consistency of VDP calculation using the same MRI scans from COVID-19 patients, but with high resolution and low (traditional) resolution versions. Using a MATLAB script developed previously, it was found that in general, using …

Numerical Simulation Of Adaptive Metabolic Response To Anti-Angiogenic Treatment In Renal Cell Carcinoma, Saranya Varakunan

Undergraduate Student Research Internships Conference

Renal cell carcinoma, a malignant kidney cancer, is often treated using anti-angiogenic drugs to prevent the growth of blood vessels within the tumour. Although tumours initially respond to this treatment, they eventually develop resistance. This resistance is hypothesized to be caused by a switch to a symbiotic metabolism that allows cells to survive even with a low blood supply.

This project seeks to computationally model the transport of oxygen, lactate, and glucose within a tumour in order to examine how cancer metabolism adapts to changes in blood vessels.

Compact Sensing Platforms Based On Localized Surface Plasmon Resonance, Zhutian Ding

Electronic Thesis and Dissertation Repository

The development of plasmonic sensors mainly focuses on the improvement of their sensitivities that are approaching the theoretical limit. This work aims to propose, fabricate and characterize compact sensing platforms that are highly adaptable and easy to be miniaturized, without compromising their sensitivities. A plasmonic sensing system that allows the excitation of localized surface plasmon resonance (LSPR) by individual waveguide modes is presented conceptually and experimentally. Another compact sensing platform is proposed based on the ensemble hypothesis developed in this thesis.

Characterization Of Cd93 Diffusion In Human Monocytes And Chinese Hamster Ovary Cells., Maria Goiko

Electronic Thesis and Dissertation Repository

The diffusion of CD93, a putative efferocytic receptor, was studied in the membrane of human monocytes and CHO cells using single particle tracking. We found that of CD93 molecules were confined in compartments consistent with actin corrals, while moved freely. Cage effect analysis showed short-lived caging of free CD93 and longer-lasting caging of confined CD93, with smaller corrals resulting in stronger caging. The motion of both free and confined CD93 was found to be consistent with a subdiffusive continuous time random walk, suggesting that CD93 diffusion is affected by several processes. We also sought to develop a total internal reflection …

A Non-Contrast Magnetic Resonance Imaging Technique To Assess Blood-Brain Barrier Permeability, Harini Pandithasekera

Electronic Thesis and Dissertation Repository

The Blood-brain barrier (BBB) regulates the entry of compounds between the blood and the brain, thus plays an important role in brain homeostasis. Studies indicate in disease states such as Alzheimer’s the BBB integrity is compromised. The motive of this project is to investigate the sensitivity of the diffusion-weighted arterial spin labeling (DW-ASL) technique to detect water exchange. Testing the sensitivity requires a reliable method of opening the barrier at specific locations of the brain. Here, a unique technology named focused ultrasound (FUS) has been used to mimic a compromised BBB environment.

A series of experiments were conducted in a …

Resting State Functional Magnetic Resonance And Diffusion Tensor Imaging Of Hemiplegic Cerebral Palsy Patients Treated With Constraint-Induced Movement Therapy: Predictors And Clinically Correlated Evidence Of Neuroplasticity, Kathryn Y. Manning

Electronic Thesis and Dissertation Repository

Hemiplegic cerebral palsy is characterized by unilateral upper limb impairment and patients often compensate by performing most tasks with their unaffected arm. Constraint-induced movement therapy (CIMT) directly combats this learned non-use by casting the unaffected arm and forcing the patient to repetitively practice skills with the hemiplegic limb. Subjects with hemiplegic cerebral palsy were recruited from Holland Bloorview Kids Rehabilitation Hospital, Thames Valley Children’s Centre and McMaster Children’s Hospital. MRI acquisitions and clinical evaluations were collected at baseline, 1 and 6-months later. The case group participated in a CIMT camp after baseline evaluations and was compared to an untreated control …

A Molecular Simulation Study On Micelle Fragmentation And Wetting In Nano-Confined Channels, Mona Habibi

Electronic Thesis and Dissertation Repository

We performed coarse-grained molecular-dynamics (MD) simulations to study the structural and dynamical properties of surfactant micelles in equilibrium and under Poiseuille-like flow in a nano-confined geometry. We used the MARTINI force-field to model the interactions between water molecules, counter-ions, and sodium dodecyl sulfate (SDS) surfactants. SDS surfactant was chosen as the standard model because of its potential application in drug delivery systems. First, we focused on the self-assembly of SDS in equilibrium. To form stable spherical mi- celles, we ran simulations in the isothermal-isobaric ensemble (NPT) on a system of free SDS surfactants, counter-ions and water molecules. We studied the …

Fabricating Cost-Effective Nanostructures For Biomedical Applications, Erden Ertorer

Electronic Thesis and Dissertation Repository

In this thesis we described inexpensive alternatives to fabricate nanostructures on planar substrates and provided example applications to discuss the efficiency of fabricated nanostructures.

The first method we described is forming large area systematically changing multi-shape nanoscale structures on a chip by laser interference lithography. We analyzed the fabricated structures at different substrate positions with respect to exposure time, exposure angle and associated light intensity profile. We presented experimental details related to the fabrication of symmetric and biaxial periodic nanostructures on photoresist, silicon surfaces, and ion-milled glass substrates. Behavior of osteoblasts and osteoclasts on the nanostructures was investigated. These results …

Fast Absolute Quantification Of In Vivo Water And Fat Content With Magnetic Resonance Imaging, Yifan Cui

Electronic Thesis and Dissertation Repository

Quantitative water fat imaging offers a non-invasive method for monitoring and staging diseases associated with changes in either water or fat content in tissue. In this work absolute water and fat mass density measurement with in vivo Magnetic Resonance Imaging (MRI) is demonstrated. T₁ independent, T₂^* corrected chemical shift based water-fat separated images are acquired. By placing a phantom with known mass density in the field of view for signal intensity calibration, absolute water or fat mass density can be computed, assuming the B₁⁺ (transmit) and B₁^- (receive) fields can be measured. Phantom …

Molecular Dynamics Studies Of Water Flow In Carbon Nanotubes, Alexander D. Marshall

Electronic Thesis and Dissertation Repository

We present classical molecular dynamics (MD) simulations providing insight into the behaviour of water. We focus on confined water, the properties of which are often significantly different from the properties of bulk water.

First, we performed several simulations investigating the handling of long-range interactions in GROMACS [1], a MD simulation package. Selection of simulation protocols such as handling of long-range interactions is often overlooked, sometimes to the significant detriment of the final result [2, 3, 4]. Ensuring that the chosen simulation protocols are appropriate is a critical step in computer simulation.

Second, we performed MD simulations where water flowed between …

Molecular Dynamics Studies Of Interactions Of Phospholipid Membranes With Dehydroergosterol And Penetrating Peptides, Amir Mohsen Pourmousa Abkenar

Electronic Thesis and Dissertation Repository

We have performed molecular modeling of membrane and peptide systems by employing the classical molecular dynamics method and force field parameterizations. In this thesis, our main interest is the interaction of sterols as well as peptides with membranes. The thesis consists of three related projects. The first project focuses on cholesterol (CHOL) and dehydroergosterol (DHE) interacting with palmitoyl-oleoyl phosphatidylcholine (POPC) lipid bilayers. We study the effects of both sterols on the bilayer and compare them with each other. We first study the condensing and ordering effect of these sterols. Then, we study their orientations within the bilayer and relate them …

Exploring Bacterial Nanowires: From Properties To Functions And Implications, Kar Man Leung

Electronic Thesis and Dissertation Repository

The discovery of electrically conductive bacterial nanowires from a broad range of microbes provides completely new insights into microbial physiology. Shewanella oneidensis strain MR-1, a dissimilatory metal-reducing bacterium, produces extracellular bacterial nanowires up to tens of micrometers long, with a lateral dimension of ~10 nm. The Shewanella bacterial nanowires are efficient electrical conductors as revealed by scanning probe techniques such as CP-AFM and STM.

Direct electrical transport measurements along Shewanella nanowires reveal a measured nanowire resistivity on the order of 1 Ω∙cm. With electron transport rates up to 10⁹/s at 100 mV, bacterial nanowires can serve as a …