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Full-Text Articles in Other Biochemistry, Biophysics, and Structural Biology
Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel
Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel
Honors Scholar Theses
Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …
Modeling Human Immune Response To The Lyme Disease-Causing Bacteria, Yevhen Rutovytskyy
Modeling Human Immune Response To The Lyme Disease-Causing Bacteria, Yevhen Rutovytskyy
Honors Scholar Theses
The purpose of this project is to develop and analyze a mathematical model
for the pathogen-host interaction that occurs during early Lyme disease.
Based on the known biophysics of motility of Borrelia burgdorferi and a
simple model for the immune response, a PDE model was created which tracks
the time evolution of the concentrations of bacteria and activated immune
cells in the dermis. We assume that a tick bite inoculates a highly
localized population of bacteria into the dermis. These bacteria can
multiply and migrate. The diffusive nature of the migration is assumed and
modeled using the heat equation. Bacteria …