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Full-Text Articles in Molecular Biology
Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega
Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega
Doctoral Dissertations
The combination of physics, biology, chemistry, and computer science constitutes the promising field of computational molecular biophysics. This field studies the molecular properties of DNA, protein lipids and biomolecules using computational methods. For this dissertation, I approached four problems involving the chemotaxis pathway, the set of proteins that function as the navigation system of bacteria and lower eukaryotes.
In the first chapter, I used a special-purpose machine for molecular dynamics simulations, Anton, to simulate the signaling domain of the chemoreceptor in different signaling states for a total of 6 microseconds. Among other findings, this study provides enough evidence to propose …
A Time-And-Space Parallelized Algorithm For The Cable Equation, Chuan Li
A Time-And-Space Parallelized Algorithm For The Cable Equation, Chuan Li
Doctoral Dissertations
Electrical propagation in excitable tissue, such as nerve fibers and heart muscle, is described by a nonlinear diffusion-reaction parabolic partial differential equation for the transmembrane voltage $V(x,t)$, known as the cable equation. This equation involves a highly nonlinear source term, representing the total ionic current across the membrane, governed by a Hodgkin-Huxley type ionic model, and requires the solution of a system of ordinary differential equations. Thus, the model consists of a PDE (in 1-, 2- or 3-dimensions) coupled to a system of ODEs, and it is very expensive to solve, especially in 2 and 3 dimensions.
In order to …
Human Decomposition Ecology At The University Of Tennessee Anthropology Research Facility, Franklin Edward Damann
Human Decomposition Ecology At The University Of Tennessee Anthropology Research Facility, Franklin Edward Damann
Doctoral Dissertations
The University of Tennessee Anthropology Research Facility (ARF) is well known for its unique history as a site of human decomposition research in a natural environment. It has been integral to our understanding of the processes of human decomposition. Over the last 30 years 1,089 bodies have decomposed at this 1.28 acre facility, producing a density of 850 corpses per acre of land. This project evaluated the abiotic and biotic characteristics of the soil exposed to various levels of human decomposition in order to determine the effect on the physicochemical properties and the indigenous bacterial communities.
Specifically, 75 soil samples …