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Full-Text Articles in 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 …
X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar
X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar
Doctoral Dissertations
We think of DNA as double-stranded helices (duplex), but the polymer exists in many conformations. Several triplex and quadruplex DNA structures can be formed in laboratory settings and exist in nature. This thesis first provides a brief description of the nature of the order in arrays of duplex DNA under biologically relevant molecular crowding conditions. Then we compare the duplex DNA mesophases with the corresponding liquid crystalline phase behavior of the triplex and quadruplex DNA analogues. In particular, we focus on G-quadruplexes. Observed in the folds of guanine-rich oligonucleotides, G-quadruplex structures are based on G-quartets formed by hydrogen bonding and …
Geometry And Thermodynamics Of Filament Bundles, Isaac Bruss
Geometry And Thermodynamics Of Filament Bundles, Isaac Bruss
Doctoral Dissertations
In this dissertation I present a study of the geometry and energetics of bundles composed of flexible cohesive filaments. This is a general class of materials, both biological and artificial, existing across many length scales. The aim of this thesis is to investigate the interdependence between the 2D organization of filaments in a bundle’s cross section, and the 3D structure, with an emphasis on the twisting mode of deformation. First we present a model of filament contacts and interactions, which we employ in numerical simulations to study the connection between the ground state energies of constant-pitch bundles and their interior …