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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 …
Optimization Of Flagellar Locomotion In The Low Reynolds Number Regime, Aidan M. Trodden, Aidan M. Trodden
Optimization Of Flagellar Locomotion In The Low Reynolds Number Regime, Aidan M. Trodden, Aidan M. Trodden
Physics
This report investigates the computational and theoretical techniques - modeled by E. Lauga and C. Eloy - used to optimize the shape of an activated flagellum for enhanced cell motility. Cell motility is ubiquitous and has a large affect on biological systems such as marine life ecosystems, reproduction, and infection. The physical principles governing flagellar propulsion are explored using computational fluid dynamics simulations, mathematical modeling, and the sequential quadratic programming (SQP) optimization algorithm. Through iterative refinement, we can identify optimized flagellar shapes that would minimize the energetic cost dependent on a single dimensionless sperm numbers (Sp). The computation of the …
Direct Parameter Fitting Of Action Potentials In Skeletal Muscle Cells Which Include Longitudinal Segments, Tyme Suda
Browse all Theses and Dissertations
Excitation of skeletal muscle cells triggers a large voltage spike known as an action potential (AP), leading to muscle contraction. Modeling of an AP is typically done using the method developed by scientists Hodgkin and Huxley (HH). In the HH method, voltage and time gated Na+ and K+ ionic currents are simulated, along with a positive “Leak” ionic current and capacitive current. Due to the complexity and the computational time required for simulation, direct fitting of HH parameters to experimental APs has rarely been attempted. A previous thesis at Wright State performed direct fitting for the case of a single …
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 …