Physical Sciences and Mathematics Commons^™

Using Molecular Dynamics To Characterize The Relationship Between Membrane Components And Dynamics And Supramolecular Organization Of Membrane Proteins, Eric Sefah

Graduate Theses, Dissertations, and Problem Reports

Molecular dynamics (MD) simulations have gained impetus as a technique for elucidating structural and dynamical information about membrane proteins (MP). In particular, coarse-grained (CG) MD simulations have provided valuable information about the relationship between membrane components and supramolecular organization of MPs. In this work MD simulations are used to characterize the effects of hopanoids on bacterial membrane dynamics and association in a model protein proteorhodopsin (PR), as well as the role of the extended C-terminus of the human adenosine receptor (A_2AR) on its dimerization. PR is found to dimerize in a manner that is dependent on both the …

Understanding The Relationship Between Local Environmental Changes And The Function Of The Ph Low Insertion Peptide, Violetta Burns Casamayor

Graduate Theses, Dissertations, and Problem Reports

Cancer is the second leading cause of death in the US with over 1.7 million new cases each year. Current cancer treatments tend to also target healthy tissues due to similarities with cancerous ones, resulting in acute side effects. Early detection is the best approach towards defeating cancer, however, modern imaging techniques require sizeable samples, often implying a late stage in the disease. One common attribute of tumors is their acidic microenvironment, which can be taken advantage of.

The pH Low Insertion Peptide (pHLIP) is a membrane-active peptide that can take advantage of the acidic microenvironment surrounding cancer cells. pHLIP …

Photochemical Motion Control Of Belousov-Zhabotinsky Droplets And Turbulence-Like Patterns In The Aluminum Hydroxide Precipitation System, Syed Jazli Syed Jamaluddin

Graduate Theses, Dissertations, and Problem Reports

A Belousov-Zhabotinsky (BZ) droplet that is immersed in an oil-phase can self-propel due to a surface tension gradient that exists on the droplet surface. The surface tension gradient is created as a result of the reactions that occur within and on the surface of the BZ droplet. By affecting the rates of these reactions, the BZ droplet direction can be controlled. In our experiments, we tune the reactions that occur within and on the BZ droplet surface by imposing a light intensity gradient on the droplet. We analyzed the BZ droplet motion and demonstrated that we can control the droplet …

Gas Phase Reactions Of Cyclopentadiene With Ch And Oh Radicals, Kacee Lynn Caster

Graduate Theses, Dissertations, and Problem Reports

The formation of polycyclic aromatic hydrocarbons (PAHs) and carbon-based nanoparticles in combustion environments is driven by the pyrolysis and oxidation of abundant fuel molecules. The subsequent growth of these pyrolytic byproducts is then propagated by reactions with small free radical species like OH, CH, O atoms, and C₂H. Cyclopentadiene (C₅H₆) is a significant five-member combustion intermediate that has been detected in many high temperature reactions, such as in the pyrolysis of jet fuels like JP-10. Experimental and theoretical investigations in the reactions of cyclopentadiene with these small free radical species are necessary towards understanding …

Modified Firearm Discharge Residue Analysis Utilizing Advanced Analytical Techniques, Complexing Agents, And Quantum Chemical Calculations, William J. Feeney

Graduate Theses, Dissertations, and Problem Reports

The use of gunshot residue (GSR) or firearm discharge residue (FDR) evidence faces some challenges because of instrumental and analytical limitations and the difficulties in evaluating and communicating evidentiary value. For instance, the categorization of GSR based only on elemental analysis of single, spherical particles is becoming insufficient because newer ammunition formulations produce residues with varying particle morphology and composition. Also, one common criticism about GSR practitioners is that their reports focus on the presence or absence of GSR in an item without providing an assessment of the weight of the evidence. Such reports leave the end-used with unanswered questions, …

Huntingtin Aggregation At Interfaces Associated With Membranes And Organelles, Adewale Vincent Adegbuyiro

Graduate Theses, Dissertations, and Problem Reports

Huntington’s Disease (HD) is a genetic neurodegenerative disease caused by the expansion of polyglutamine (polyQ) domain within the first exon (exon1) of the huntingtin (htt) protein. Due to this mutation within the polyQ domain, htt aggregates into various toxic species such as oligomers, fibrils, and other amorphous aggregates. While the aggregation of htt strongly correlates with polyQ length, other factors, e.g. interaction with membranes or organelles and posttranslational modifications (PTMs), modulate aggregation. The first 17 N-terminal amino acids (Nt17) that precede the polyQ in htt-exon1 enhances aggregation and facilitated binding of htt to membranous organelles, promoting morphological changes and disfunction. …