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Statistical, Nonlinear, and Soft Matter Physics Commons™
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Articles 1 - 3 of 3
Full-Text Articles in Statistical, Nonlinear, and Soft Matter Physics
Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost
Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost
All Dissertations
In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …
Long-Range And Chaotic Active Mixing Of Swimming Microbes In A Vortex Chain Flow, Nghia Le
Long-Range And Chaotic Active Mixing Of Swimming Microbes In A Vortex Chain Flow, Nghia Le
Honors Theses
We present experiments studying the motion and active mixing of swimming mi- crobes in laminar, vortex-dominated fluid flows. We are testing a theory that predicts the existence of swimming invariant manifolds (SwIMs) - invisible, one-way barriers blocking the paths of self-propelled tracers in the flow in one direction. We also pro- pose that the SwIMs together can form chute structures in three-dimensional phase space that facilitate cross-vortex transport of the microbes. We also observe evidence of how these structures promote long-range transport at different non-dimensional velocities (microbe’s velocity relative to flow velocity). Long-range transport is quan- tified by measuring the …
Giardia Lamblia Growth In Viscoelastic Fluids, Kelly Watanabe
Giardia Lamblia Growth In Viscoelastic Fluids, Kelly Watanabe
CMC Senior Theses
Giardia lamblia is a single-celled protozoan parasite that when ingested, causes diarrheal disease and infects 33% of people in developing countries. Previous studies observe Giardia in water-like fluids, but Giardia's infectious environment consists of viscoelastic mucus in the small intestine. Therefore, Giardia was cultured in viscoelastic fluids, and its population growth was observed in vitro. To create shear-thinning viscoelastic fluids, 0.2% and 0.4% long-chain polyacrylamide (LCPAM) was added to cell culture media. Giardia was cultured in control media, 0.2% LCPAM, and 0.4% LCPAM, and population growth was quantitatively determined over time. Increasing LCPAM concentration resulted in a solution with …