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Molecular Dynamics Studies Of Nucleic Acids And Ribonucleoprotein Complexes, Tyler James Mulligan
Molecular Dynamics Studies Of Nucleic Acids And Ribonucleoprotein Complexes, Tyler James Mulligan
Master's Theses and Capstones
Molecular simulations of protein-nucleic acid complexes, as well as the HIV-1 Trans Activation Response Element (TAR) RNA molecule, were conducted. First, three different molecular dynamics techniques were studied on the molecule HIV-1 TAR RNA. The three techniques studied were classical molecular dynamics, steered molecular dynamics (SMD), and metadynamics. The classic molecular dynamics simulations were used to equilibrate the HIV-1 TAR RNA system, as well as every other system studied in this thesis. The SMD technique was used in order to observe the breaking force of the nucleotide interactions within TAR. This breaking force averaged to about 100pN. The metadynamics technique …
Distinct Types Of Electron Distributions Functions In Magnetotail Reconnection: Implications For Particle Energization, Guanlai Li
Doctoral Dissertations
Magnetic reconnection converts energy stored in magnetic fields to plasma kinetic energy by accelerating and heating the plasma, and is believed to be the underlying mechanism of many energetic phenomena in space. Electron distribution functions exhibit the effects of electron energization by the reconnection process. Using CLUSTER data, we have studied electron distributions in the inflow and outflow regions of magnetotail reconnection. Based on comparisons of CLUSTER measurements with PIC simulation results, we discuss the energization mechanisms. The inflow electron distributions can be characterized by their temperature anisotropy into three distinct categories: (1) anisotropic with Tepara>Teperp, (2) isotropic with …