Biological and Chemical Physics Commons^™

Multiscale Network Modeling Of Native And Modified Photosynthetic Light-Harvesting Complexes, Zane E. Armijo

Chemical and Biological Engineering ETDs

Photosynthetic light-harvesting complexes harvest solar energy and direct electronic excitations toward reaction centers with exceptional efficiency. This dissertation models the Fenna--Matthews--Olson complex of green sulfur bacteria, coupled to the PscA1 reaction center, as a chromophoric network. Forster resonance energy transfer theory, validated against numerically exact hierarchical equations of motion, was implemented in kinetic Monte Carlo simulations to resolve fine-grained excitation-transport pathways. The predicted charge-transfer efficiency of 77\% agrees with experiment, with the FMO2 monomer and its gateway pigment governing interfacial transfer. Systematic single, multi, and symmetry-preserving site removals, interpreted through Mobius inversion, identify critical pigments and show that cooperative effects …

Heterochiral Dna Nanotechnology For Biomedical Applications, Tracy L. Mallette

Biomedical Engineering ETDs

In the past 30 years, there have been major advancements on how to treat and diagnose disease because of the improvement and increase in accessibility of sequencing technology. Nucleic acid-based therapeutics can manipulate protein expression. Likewise, pathogens can be identified and detected with single nucleotide specificity. However, the underlying oligonucleotide technology requires protection against natural defense systems that have evolved to destroy foreign nucleic acids. Many chemical modifications that can protect nucleotides also have significant cytotoxic side effects and must be carefully designed into the strands. A novel way to protect against nuclease-mediated degradation is through the use of mirror-image, …

Computational Investigation Of The Interactions Between Bioactive Compounds And Biological Assemblies, Tye D. Martin

Biomedical Engineering ETDs

Small, biologically active molecules with unique properties and applications are potential solutions to a wide range of threats to global health including infectious agents and neurodegenerative disease. Experimental studies on a class of oligomeric p-phenylene ethynylenes (OPEs) have shown potential both as bioactive antimicrobials and fluorescent sensing agents for tracking amyloid-β (Aβ) aggregates found in Alzheimer’s Disease (AD). A second type of small molecule with potential applications in AD therapy, curcumin, has been found to interfere with Aβ fibril growth. Curcumin also attenuates Aβ-membrane interactions and Aβ toxicity. Our goal has been to use computational techniques to better understand the …

Topics In Three-Dimensional Imaging, Source Localization And Super-Resolution, Zhixian Yu

Physics & Astronomy ETDs

The realization that twisted light beams with helical phasefronts could carry orbital angular momentum (OAM) that is in excess of the photon's spin angular momentum (SAM) has spawned various important applications. One example is the design of novel imaging systems that achieve three-dimensional (3D) imaging in a single snapshot via the rotation of point spread function (PSF).

Based on a scalar-field analysis, a particular simple version of rotating PSF imagery, which was proposed by my advisor Dr. Prasad, furnishes a practical approach to perform 3D source localization using a spiral phase mask that generates a combination of Bessel vortex beams. …

Combined High-Speed Single Particle Tracking Of Membrane Proteins And Super-Resolution Of Membrane-Associated Structures, Hanieh Mazloom Farsibaf, Keith A. Lidke

Shared Knowledge Conference

Many experiments have shown that the diffusive motion of lipids and membrane proteins are slower on the cell surface than those in artificial lipid bilayers or blebs. One hypothesis that may partially explain this mystery is the effect of the cytoskeleton structures on the protein dynamics. A model proposed by Kusumi [1] is the Fence-Picket Model which describes the cell membrane as a set of compartment regions, each ~ 10 to 200 nm in size, created by direct or indirect interaction of lipids and proteins with actin filaments just below the membrane. To test this hypothesis, we have assembled a …

Ion Size Effects On The Properties Of Charge Regulating Electric Double Layers, Divya Jyoti Prakash

Nanoscience and Microsystems ETDs

The behavior of charged interfaces formed in various systems like colloidal solution, fuel cells, battery, electro-deposition, catalysis is governed by the properties of electrical double layer(EDL). Civilized model with charge regulation boundary condition determined by thermodynamic equilibrium at the interface has been used to model electrical double layer and shows that size of the solvent plays a critical role in characterizing the properties of EDL using classical density functional theory.This thesis investigates the impact of ion size in electrolyte solutions on the electrical double layer formed at the interface using a similar model. It is found that ion size greatly …